input shaft bearing would have noise in all gears. as 4th and 5th have no noise, i'd be looking at counter shaft bearings

The more torque that goes through the gearbox, the more side load there is on the input bearing.
That's why it starts out loud in 1st, as the high ratio tries try to push the gears apart, then it gets subsequently quieter with 2nd and 3rd, then no noise in 4th due to no power being transmitted through the counter shaft (no side load at all).
There probably is some noise in 5th, but it would be less again than in 3rd, and it probably can't be heard due to road noise at that speed.

Theoretically it could be the front counter-shaft bearing because it would see the same side loads as the input bearing.
The difference though, and the reason it will be the input bearing, is because of how the main-shaft is split in two pieces. Through the gearbox's life the pre-load on the main-shaft would be reduced and would allow the two parts to deflect a little which would take the input bearing slightly out of alignment and put a higher load on it causing the damage.

Thanks for the replies guys,

both of mine are WC as they're both out of EL's and they both have the distinctive pin on them. I'm going to do some research into a rebuild and see if it's feasible in my current financial situation haha.

i'd like to rebuild the old one and considering the noise the one i just installed has settled down a bit to a very dull whine now, its not really even annoying me anymore, i don't know if that's better or worse but i'd like to think it's the bearings and gears all getting the fluid through them and running a tad smoother as the gearbox i put in had been sitting out of the car for a while i think...