1. You can get purify runes mostly from events, also cave exploration (cave keys) have a chance of dropping them as well. I haven't really tried farming purify runes so someone else may have more information. Credits to ICE* for the following thread links. Go here for more information:

https://forum-narutoen.oasgames.com/page/show-post-29334-1.html

2. I believe with the purification system, you can reach up to a maximum of 100% with a single purification, which is very very rare. (Having in between 90-100% is considered very good already) there is also a way to get even higher, but you must obtain Breakthrough pills which give an extra 1% for the stat (I think) and you can stack up to 20 pills on each equipment (Allowing a max up to 120%), however breakthrough pills are often very hard to obtain or are very expensive (Probably in the range of 10-20k, but aren't worth it as they give a tiny amount of power)

3. Cave Keys have become super easy to get with the new storage room system. Before they were fairly difficult to obtain in large quantities. The main way of getting them are from events and wishing tree. You c*so purchase packs of 88 keys for a decent price but only if you really want them

More info on Cave Keys: https://forum-narutoen.oasgames.com/page/show-post-29641-1.html

4. They charms system can be found in the strengthening tab. It works a bit similarly to the refinement process except each piece of equipment has a corresponding charm. Charm Packs are the main way of obtaining charms, they drop 1 type of each charm and cost around 100-125 coupons. You can obtain Charm Packs from a bunch of different events so they aren't too rare. Rescue Jinchuriki (an event) also gives 1 charm fragment every time you participate (10 charm fragments for a charm pack) and doing Ultimate Training also rewards you with 6 charms of a single type.

More info on Charms: https://forum-narutoen.oasgames.com/page/show-post-29032-1.html

5 (Summon Cultivation). So Mystery Gems can be obtained through the group shop via the Redemption Market and I believe they cost 250 Group Coins, which is fairly cheap. In order to spend Mystery Gems however, you must first obtain the Summon, then get their summon cultivation to the appropriate level where their summon mystery is unlocked, It'll be on the top right of the cultivation panel. Once you unlock their mystery, each different summon mystery has 3 tiers. Each tier provides increasingly better buffs but cost more gems and some may require other items. As for upgrading summon cultivation, I would try to upgrade them about evenly to reduce the cost of summon cultivation because they get very very expensive past Tier 4 Cultivation and by upgrading cheaper cultivation, you can upgrade your summoning level so that you unlock a greater variety of summons to upgrade.

More information on Summon Mysteries: https://forum-narutoen.oasgames.com/page/show-post-31071-1.html

6 (Summon Runes). So Summon Runes are fairly easy to get now, the main way that you obtain them is by drawing in the Summoning Treasure using Summoning Scrolls, this generally gives you most of the summon runes that you will use but you c*so buy summon runes from the Summon shop using Summoning Points that you get from duplicate summons

7 (Group Summon). Group summons are a feature that allow you group to fight a group "boss" two times every week. The rewards that you get from the boss are determined by the amount of damage you deal to it. Its basically a miniature 9-tails event but only for your group. When you first join a group, the summons will be locked (There are currently two summons), I believe that you will only be able to fight the Gamabunta Boss after you obtain the Serpent Group Summon. In order to obtain group summons, your group must first fight the boss to obtain summon fragments for the appropriate summon. After you collect 200 (I think) summon fragments, you will be able to unlock the Group Summon. After you unlock a group summon, they will provide buffs to your entire team. The buffs that you get from a group summon is determined by the group summon level and the current summon %. Starting off with the group summon level, you can upgrade your summon by spending Group Funds and Summon Chakra. To obtain Summon Chakra, you sacrifice chakra runes you get from Chakra Packs that you get from daily practice. However, the buffs that you receive in the end is ultimately determined by your group summon % which is the exact same process as upgrading your summon but summon % decreases a certain amount everyday, and so you have to keep on feeding your summon in order to maintain the full effects of the buff.

8 (Treasured Tools). Yes, you can get S tools without a blueprint, I believe the drop rate is somewhere between every 21-28 scrolls, so if you draw daily, you'll get one in 3-4 weeks. As for scrolls, you get those in the ability treasure and they drop occasionally, I'm not sure the drop rate but they aren't super rare. You should also obtain a few free scrolls at the beginning I believe. For scroll points, you one every time you draw from the ability treasure, this includes free draws, so you can obtain them without spending. This is also another method of getting higher level scrolls that you want.

More info on Treasured Tools: https://forum-narutoen.oasgames.com/page/show-post-28517-1.html

9 (Mt.Myoboku). A very very very very long time. Theres also two versions of Mt. Myoboku, oil cultivation and balance training, however they work the same way just have different items to unlock each path. Read here for more information:

More info on Mt.Myoboku costs: https://forum-narutoen.oasgames.com/page/show-post-33018-1.html

10 (Assist links). The main way of obtaining scrolls was from the Sun shop but were event last week that were selling them for 55 each, so if you don't want to spend sun scrolls on them, then you should probably spend in that event as its also worth it.

More info on assist links:

https://forum-narutoen.oasgames.com/page/show-post-33417-1.html

https://forum-narutoen.oasgames.com/page/show-post-33393-1.html

https://forum-narutoen.oasgames.com/page/show-post-33705-1.html

11 (Ninja Breakthrough). With the recent update, this feature has become a little bit more complicated, but I'll start from the beginning. I'm going to start by explaining what skillbreaking is and why its good. Skillbreaking is normally available to ninjas who have stronger counterparts. For example, there's the normal Sasuke, but then there is also Sasuke [Susanoo]. Because you can only have one of the same ninja in your team, and Sasuke [Susanoo] is much better than the normal Sasuke, it pretty much makes the old Sasuke obsolete in mid/end game. This is where skillbreaking comes in hand. Skillbreaking allows older ninjas with better counterparts to have a chance of becoming the meta by improving their old skills. So before you can skillbreak a ninja, you must first get them to 4 stars (With a few exceptions like Tobirama and Hashirama). Once they are at the appropriate level (I'll be using 4* for the sake of simplicity), you c*e skill books to get their breakthroughs. There is also another method but I'll get to that later. So skill books can be obtained in 3 ways, the first is to purchase skill books with coupons, in certain events, however i believe this option is only available to Tobirama and Hashirama, but I could be wrong. The second way is to get the for free from Mt.Myoboku Trial event when it comes around every once in a while. During this event, you have to sign in everyday to receive a reward and sometimes they have skill books as free rewards, especially after they release a new skillbroken ninja. The final way is to get skillbooks by trading in extra ninja fragments for the skillbooks. The costs vary from each ninja and different skills may cost different amount of fragments, but this is one of the main ways of obtaining more common ninja's skillbooks. However, now with 5.0 out, there is also another way of skillbreaking a ninja and its with the Skill Trial feature and I should point out that this feature is currently limited to Sasuke and Tsunade [Sannin War]. This feature allows you to use Experimental Vials in order to unlock different skills for the ninja, similar to the purification feature (kinda). However, this feature also adds the Y variants to skillbroken ninjas. Y varients is basically another path that the ninja's skill can take. Think of it like choosing talents for your main. Instead of being forced to choose a single type of mystery, you now have the ability to choose between two types of mysteries. While this feature is slightly more complicated than that, it's not too difficult to learn with some experimentation with it. Also you can get experimental vials from events and Team Ninja Exams.

12 (Mood Scrolls). Yes and No. So mood scrolls are still fairly difficult to obtain without spending coupons but they aren't super rare. Especially with the new Great Plates event that has quickly become one of the best events in the game which rewards a large quantity of Mt.Myoboku Scrolls/Oils and Mood Scrolls

13 (Tactics). Tactic pages can be bought from the shop for 25 coupons each, however the method that I used to get my tactic pages are were from the Mt.Myoboku Trial event which has a wheel that you can spin which occasionally gives you the Tactics Optional Pack which lets you choose 10 tactic pages from any tactic. Spinning the wheel only costs 100 coupons so it's a great deal

14 (Elite Instance). Most common ninjas can be found in Elite Instance, but a decent amount c*so be bought with the Ninja collection system that was released in 5.0, you get coins from doing Survival Trail and can spend them to get ninja fragments, similar to the old 4.0 feature

15 (Super Rares). Super rares are still difficult to obtain but they are definitely obtainable as a f2p. I myself am a F2P and I saved 5 months for Shisui and I'm still very happy I did so. Honestly, you don't need very many super rares. If you can get a good one that lasts you for a while, then there is no reason to drop a bunch of money on a ninja who's been hyped up and recently released and then find out you don't use him later on.