Have a 94 4Runner 5speed looking at buying a low mile 2.4 out of a 96 Tacoma, has anyone done a swap like this? My biggest concern is trans lining up and wiring going together

 

Do you have a 22RE or a 3.0 currently?

 

Why swap the smaller 2RZ 2.4? Might as well do a 2.7 3RZ.
There are some variations with the 2RZ that can be a PITA unless you get the donor vehicle.
You will need the matching bell housing

 

Right now I have the 3.0 and it is running fine I just found a good deal on the motor it's in a totaled 96 Tacoma with 80k miles on it for 300 bucks with transmission so it's a deal and I'm gonna take it and when the time comes when my 3.0 (with 190,xxx miles) decides to lay down I will have a swap ready

 

Pass on the 2.4 and save the money until you find a good deal on the 3.4 v6. Much easier swap for you.
https://www.yotatech.com/forums/f159/

 

He is dead on. The 3.4 swap is a pain but at least it will bolt up to your transmission and you don't need to move your engine mount locations. Going from a 3.0 to any thing is a pain but the 3.4 is probably the least fab work.