Original:
So I have had an ongoing issue with my 2005 3.0R-B 6MT, on acceleration a vibration can be felt through the car when accelerating through 2000-3000rpms, peaking around 2500rpms. This only happens under load, e.g. going up a hill in 1st and 2nd gear on moderate acceleration, straight or corner. This does not happen when going downhill and is less noticeable on a flat road as the revs increase quicker with less load on the driveline.
Update; 7 May 2017
Summary:
Driveline vibration occuring randomly, most noticable in 3rd gear at 30-40kmh, medium throttle. (Problem was getting worse, to a point where full acceleration in 3rd gear above 4k rpm caused intense shaking of the whole car.)
After replacing all engine and transmission mounts, having the tailshaft repaired (u-joint replaced and tailshaft balanced), fitting different wheels, changing spark plugs and having multiple retunes etc. my problem was solved by replacing both front driveshafts. The car now accelerates better than before and no longer struggles/stumbles through the 2-3k rpm range.