Travis, I'd be able to help out directly with mastering if needed. I can help directly with mixing if it happens to be the same program I use or if he is willing to do a stem bounce. I could also give general EQ and mixing suggestions for him to use.
As for #2, it's not about note placement as much as it is about EQ and compression, likely.
#3 for patches, I'm sure there's lots of programs out there. If you're talking about what's included in cakewalk, then I haven't got a clue. But I'm sure there are some cheap programs out there with this option. If need be, I can maybe run some of it through my own software.
#4 this sounds like a soundcard issue to me. Make sure you are running ASIO drivers and have an ASIO capable card. Last I check (which was a while ago), pro audio software and native windows drivers do not get along well. I'd also suggest increasing the audio buffer and making sure you have a well organized, fast hard drive (or a solid state drive, which works wonders).
Listening to the MP3s, I'd also recommend he lay off the single band compressor a bit, I can hear it pumping.
I think the compositions are good and the game looks great in motion.
If you want to get in touch, you can email me at NHC at Bubblepipemedia dot com . See same site for examples and more information.