High flow cats don't exist, or I should say that all cats are high flow. The "high flow" label is a myth/gimmick to prey on consumers. Buy a cat based on construction quality, not flow, because they all have little to no restriction.
TB spacer does nothing.
If you're boring your TB to 62 mm, you better be boring your intake manifold too. If you don't want to bore the manifold, 60 mm is the limit for the TB and should be plenty unless you're really dumping a ton of money into a stroker/forced induction build.
Banks headers are nice, but really not an ideal setup (no one makes a very ideal header for 4.0 performance) and as such aren't worth the money over something less expensive such as APN imo. I'd love a header with equal-length, narrow primaries that collect 6 into 3 pairing cylinders 1+6, 2+5, and 3+4, but no one makes anything like this to my knowledge.
Like the poster above said, you can throw a bunch of money at your 4.0, but you won't get ton out of it. The 4.0 is pretty well tapped for power from the factory. Stroking it gets good gains, but then again, once it's stroked, it's not a 4.0 anymore (it's a 4.5 or 4.7 or 4.9 or whatever) and is still maxed-out for whatever its new displacement is. Forced induction provides gains but is super expensive.
A nice 2.25" or maybe 2.5" exhaust with a header is the best bang-for-buck you can do imo. CAI can contribute a little after that. Replace your mechanical fan with electric to free some power. If you want to throw even more money at it, stroke it and/or consider port/polishing the head and shop around for a cam that will give you the kind of power curve you want.
Build Thread -- http://www.jeepforum.com/forum/f177/whats-chrokeese-build-thread-2525690/