SH3+Commander+GWX3 all work wonderfully together, the jonesoft.txt file I would guess is from the mod enabler - JSGME - as it's just the text file I'd ignore it but now you seem to have made it worse.
If it was me at this point I'd uninstall everything (sh3+mod wise, including stuff in My Docs. folder), then run a registry cleaner and install fresh.
Read through the install details for SH3 (get rid of StarForce! - see the installing on Win 7 thread), JSGME and GWX, follow them to the letter and you shouldn't have any more problems.
Once you're up and running with GWX I don't think (but will no doubt be corrected if I'm wrong
) that you need to do the academy stuff again.
If your native resolution is 1920x1080 and the game is fine with that why try for another resolution, especially one your monitor wasn't designed for? (Edit, just read Pisces' post above. Ignore me.)
Very important -
bin the X-1 stuff! Don't let anyone else get their mitts on it.
Finally, for now, welcome aboard 