Is it possible to have Hand stack size of 250 NOT increase with research?
Only a problem when loading higher stacksize items like ash.

I'm aware of the issue, and unfortunately, there is no good solution for it: it's impossible to exclude inserters (cranes) from being affected by bonuses. As a workaround, you can explicitly set the stack size (250) in the blueprint and use that blueprint for placement.

If you want i can send a script that changes stack size for already placed cranes.

Can you post the script here, I have a lot of cranes that I need to fix

Update mod and check startup settings, hope it's helpful :)