T50 weird gear set What´s going on?

[Bean]

well feel wise it's true the gap from 3rd to 4th is bigger than the gap of the other shifts. BUT the gap itself is no different than stock. If you really have the TRD 3 kit and coming from a stock gearbox the main change, aside from the 1st and 2nd being higher than stock (therefor closer ratios) is the fact that in the stock gearbox the gaps between gears is getting smaller (1st->2nd biggest gap, 2nd->3rd a bit small, 3rd->4th smaller again, etc) - this is also the case with the TRD 5 kit. As this got a shorter gap between 3rd and 4th than stock, we can rule it out though.

the final drive changes NOTHING on the gap between gear. Fitting a shorter 5.3 will only yield less speed, for the same engine rpm, and hence more torque at the wheels, compared to the 4.3 (think of it like fitting really small (smaller overall diameter) wheels to the car)

I'll see if I can butcher together the gear graphs in PS to make it more visible what I described above.

As said going back to your initial statement IF your rpms drop the amount you mentioned AND are correct - something is off/strange.