The chip ram mod should be fine to do, and is generally beneficial - the only exception might be with old software that's expecting fast memory in that address space, or I suppose if you try to do the mod and don't have the right Agnus chip installed, or have done it wrong some other way.
I'd point the finger more at all those cracked versions of games you mention trying, rather than anything else. I bet if you boot it to Workbench it would be perfectly stable.
Also, you might want to look into either a Gotek or WHDLoad for your miggy. Floppies suck.
lol
