no mk2 box isnt any stronger, just the mk3 tends to kill them quicker. I guess its down to the weight, usually its the reverse gear that goes 1st, mk3s have a real problem with chipped gears.
anyway yes it will fit, just make sure its a 1.8 box so it has the 100mm driveshaft flanges. If you arnt planning to swap the clutch kit check the gearbox code of the box you have, if its a 16v 2y box the input shaft on the box will be bigger so the clutch will only work with a MK3 2.0 8v box or another MK2 16v. If you are swappign the clutch just get one to match whatever box you find, MK2 8v = 8v GTI clutch kit, 16v = 16v clutch kit