On my user manual it says magna tj 2002 has a different gearbox to a magna 2000 tj ...but all the numbers off the TJ 2002 box i wanna buy are the same f4a51k2b5b mh9889...just wonder if i will have any issues ?

Will fit

Firstly, wrong section mate. This is the 1st gen section. The 96-2005 Magna's are third generation magna's.

Secondly, provided you're doing a swap between gearboxes with the same amount of gears (e.g. 4sp to 4sp and 5sp to 5sp) you should be fine. Especially if it they're both TJ's. Straight swap.

ok cool thats great news