Hey FoneBone, Interesting patch BTW. The MacBookPro has an audio interface (line in which you are using), albeit crappy, they all are (why we spend the $s on decent I/O devices). So yes a better I/O would help/be better, but would need to be USB or apple stuff??
That said, you should be able to get reasonable results with what you have.
Lets break it down:
MP1 A out > GCS-2 > MBP line in. So mono from MP1 to GCS-2 and mono from GCS-2 to Line in (line in is stereo, if the mini jack you are plugging into the MBP is mono ?? then try pulling it out a smidge, then the tip goes to left and right line ins ( suspect this is your main problem for now ?), otherwise it goes to one channel only and can cause noise/not sound good issues). So what will be recorded (sent to MBP) is MP1 and left channel of inteleflex (depending on MP1 loop setting)
What you listen to though, through your cabs, is stereo version + BBE (which is not being recorded).
Question ? when you play something back from your MBP what do you listen to/through ?
A "better?" recording patch to try: GCS-2 in MP1 loop (turn on loop/GCS-2 when recording) > MP1 A/B to Intellifex L/R > BBE L/R > (2x mono jack to stereo mini jack) > stereo MBP line in for recording.