A basic tell tale on auto condition is the colour and smell of the oil. You're actually meant to service autos every 12 months 20000kms to maintain them well.
The turbo boxes can be built strong you've just got to do it right
http://www.skylinesaustralia.com/forums/topic/290880-rb25det-gearbox-crunching-into-4th-gear/page-3?hl=%2Brb25det+%2Bgearbox+%2Bcrunching#entry6033953
has some pictures. But yes you need a couple of different size pullers and a bearing press
Solid diff mounts increase the amount of NVH throughout the car, i would be checking all the bushes in the back end and your diff. Grab the diff yoke and move it up and down, 1 of the pinion bearings starting to fail will cause a bad vibration also