I never really thought about it, but how much trouble do you guys think I'd have if I tried to take off a custom made intake and exhaust off of the N/A and put in on the 1JZ during/after the swap?

what are you trying to say????

If you have a "general" K&n cone and you clamp it to a pipe that routes up to the 1JZ intake "split"/T, I imagine it will work fine.
If your cat-back is made to bolt up to the stock main cat location, it will work with the 1JZ. Unless your piping is 3" and mandrel bent, I wouldn't really suggest it though.
Trust MX front pipe, 3" test pipe and a 3" cat-back should do you well.

Thanks DM. I'm planning on getting an A'Pexi filter, then doing custom intake piping, as well as custom 3.5" stainless steel exhaust tubing. Wasnt sure if I should be careful when I bolt them up, but I think I might just do the intake and wait till I do the swap before I get an exhaust upgrade. Theres plenty for me to be had during/after the swap: A/F gauge, turbo timer, boost controller...

Edit: This isnt the same webpage that I found the info on, but its the same test. Check out each different filter: http://www.mkiv.com/techarticles/filters_test/1/index.html

Edit: This isnt the same webpage I based my info on, but it was the same test I believe.

http://www.mkiv.com/techarticles/filters_test/1/index.html