going to accel coil packs isn't going to increase the power, the stock ignition system is plenty.
header won't gain you much either, the stock manifold is a decent setup.
getting rid of the air muffler in the intake should get you a little more grunt on the top end though, it will make it a little louder but you probably don't care... the stock air filter is the same as on a 4.0L, so it's not as restrictive as you would think if it can flow nearly twice the air a 2.3L needs...
if you think you need a less restrictive intake, get a vacuum gage and plumb it up to the engine, drive down the highway and floor it, the gage should point directly at 0, if you are still at a couple inches of vacuum then you are being restricted.
I'm running a turbo 2.3 through the stock intake plumbing and exhaust system (including cat), sure it's not the optimum setup, but it runs fine most of the time...