Hmm, well yes, you want to stick with as many ints as possible. The math is processed faster for them, and they take up less space.
There are a number of routines you can erase from the default code. Mainly, I would read through the Default_Routine sub and then clear it out.
Depending on your method of executing auto mode, you could be eating lots of memory. If you're doing it case-by-case with lost of IFs, or a switch or something, that needs to change. The method I use is to hold an array of movement data and then have a small piece of code that executes it. It works fine, and you can have some massive arrays too.
It also sounds like something might've gotten modified that shouldn't have...
We had someone do this on our team and we had memory problems too. We had to restart from scratch from that point.