You've probably found some of this out for yourself, but some notes on compiling AMOS Pro from the original sources:
+W.s must be assembled with the -C option to force mixed case recognition.
+Lib.s has a leftover "illegal" instruction in the original source (line 4,541) presumably from a debugging session.
If you're using GenAm V3.02 (the one that came with the sources) "illegal" bit numbers should be okay. If you're using GenAm V3.18 (recommended!) you'll need to include the line
OPT NOCHKBIT
for any sources that use "illegal" bit numbers in lines like this one:
btst
#13,DmaConR(a6)
That prevents the heaps of warnings you'll get from the likes of +W.s.
All the necessary files should be in the original sources and in the beta V2.10. So you can ignore the stuff in the JBB_Graphcics folder, etc. Note that V2.10 is still under development so expect a lot to change. Source synchronisation could get very interesting...
Above all, note that AMOS Pro does things within its own system architecture. So any changes have to be carefully considered against the effects on "the way AMOS does it", otherwise disaster awaits as the code is very tightly coupled in places. Your other thread on how to get the editor to scroll from a wheel mouse is a good example. Don't hack it! Incorporate it into the tables already used for handling keystrokes and functionality. That way, macro compatibility, scope, etc. is maintained and easily changed without resorting to much by way of code changes.