The mounts only have about 2000 km's on them. But there is a good chance that maybe some damage was done prior to them being replaced.
I have noticed the increased vibration from 800-1200 rpm you mentioned, that doesn't bother me and i'm assuming is just resonant frequencies from the stiffer mount set.
The clutch is an unknown for sure... it has never been replaced by me.. and i've had the car since 192000 km. I would assume if it was the clutch that it would affect all gears.
Finally, under heavy engine braking (i.e. hard accel up to redline in 1st, release gas, there is no odd vibrations, it only seems to be under accel)
Thanks for the all the good points though, I'll take a look into the tranny mount and guibo when I can get under the car next.