Here is how init works in survival, it works this way from day one of the game and it won't be getting changed, so there is nothing to fix you just have to get round the system.

Your enemy has his normal stats, as is show on highscores.

To find out your stats remove your ninja tools, and your init together, then divide it by 4. This will be your init on every position in survival + the ninja tool you add on it

For example you have 6000 + 5000 + 11000 + 7000 init without ninja tools, that will be 29000, divided by 4 you will have 7250 on every position, add your best ninja tool for 3000 and you will have 10250 initiave in survival, while normaly you would have 11000+3000 = 14000. This is why you are slower on move 1 but probably faster on rest, because it evens out your initiaitive, it also works exact same way in matsuri and in arena but in those modes it also evens out your oponents init not just yours. Pretty much everybody who stack their move 1 a lot will notice this in survival at one point.