I was merely running a headphone jack from the headphone-input to the
computer's "line-in" jack, and the radio never had to be above "4" in
volume (it maxs at 30) to get this clean maxed out signal.

But after this reformat, my original settings no longer work, and I
don't know if there were other settings that needed to be changed. But
for right now, when i record, there is a very obvious buzz from the
amp. help!

radio shack makes a stereo isolator (aimed at car stereo problems) with the
appropriate adaptors it probably will take care of you buzz or hum issues.
likewise any pair of good transformers, correctly wired or pair of passive
DI boxes (as used by musicians)

the di boxes usually have a 4:1 step-down ratio might be the best thing to
help match the levels.

make sure toy radio outputs are still functioning correctly by inserting
headphones and listening.

make sure your patch cable has not shorted.

always check the easy problems first!