Hmm ... you must have written one heck of a program there. I've written VBA Excel applications over 3000 lines long with quite intensive calculations (looping etc.) and have not encountered this problem.
Instead of creating different files, have you tried placing related elements of code in different modules. In my 3000+ line example I have about 10 modules.
Another thing that is not obvious (because you can't see it) is that the VBA editor seems to keep a history of everything that you have done - this can also cause crashes. You can clean up your code using click here - this works with later versions of Excel.
I suggest that you try the code cleaner first. If this doesn't work feel free to click on the envelope to send me a message