I could really use some help on this one! Here's the basic info:

1997 Wrangler Sport 4.0L, only mods are 10.5X31 tires on wider 15" wheels. 139,XXX miles, just bought it a couple of weeks ago from first owner. It had been sitting for approx. a year unused, but drove fine on the test drive etc. Commuted to work in it (90 miles round trip) a couple of times, no issues.

Decided to do basic maintence on it since it had been sitting:

1. Did basic maintenance, changed oil/filter, changed air filter, ran Lucas injector cleaner through a couple of tanks. Replaced, plugs with new Bosch Platinums. Took it on a long weekend road trip and got a check engine light after a burst of hard accleration in 2nd gear to 4900 RPM or so. Jeep still ran fine, just CEL on, so drove it home (4 hours). Checked codes at home with OBDII scanner, got misfires in cyl #1 and cyl #4. Cleared codes.
2. Replaced wires, cap and rotor. Read about these Bosch single platinum plugs not being great in the 4.0L after researching first misfire codes, so replaced again with Autolites, gapped to .035.
3. Distributor cap screws rusted and broke off in distributor housing, couldn't drill out successfully = new distributor. Replaced distributor, the Jeep ran and drove, but ran rough, was probably a spline or so off. Had a friend come over and we did the distributor replacement from scratch, marking housing, finding TDC etc. Fairly confident distributor is in correctly now, but still idles rough and has valve tapping noise when on the throttle. Repeatedly throws the Misfire Cylinder #4 code, even if taking it easy.
4. Cleaned throttle body, and removed/cleaned/replaced IAC. Still runs rough, meaning it idles like it's got a big cam in it. Exhaust pressure at tailpipe pulses. Still throws cylinder #4 misfire codes.
5. Hooked up a vac gauge to the brake booster line off the intake manifold and the needle stays in the middle of the green "good engine" range on the gauge at idle. It does however tic back and forth slightly, not a big fluctuation, imagine a hand on a clock ticking 1 second forward and backward off the dead center point of the green range on the gauge. The ticking matches the way the motor 'lopes' like it would with a big cam.
6. Used Seafoam to do a top engine cleaning, ran it in through the throttle body.  No improvement.
8. Found a small hole in exhause at bottom of downpile, got it welded closed. No change (except no more exhaust leak noise)
7.  Changed coil, misfire now shows up more on cyl #3 and #6, and also, when accelerating slowly with even throttle presure, I can feel the jeep hesitate slightly.

I don't know what to do next here.  I'm not sure what is causing the misfires and why it moved to a different cyulinder(s) with the coil replacement.  It still idles rough and feels down on power a bit.  I can still hear a valve tap type noise as well, but it had that at the time of purchase and ran fine.  I'd appreciate any thoughts on this.  

Is it a new distibutor? Good bushings, no play?

Here is some other stuff from the Factory Service Manual:

Some times, problems in the fuel delivery system can cause an erroneous mis-fire indication by the PCM.

Fuel pressure test (SB 49.2 psi +- 5 psi)
Fuel pump volume test (.25 litre in 7 seconds)
Leak down test. (Most common cause of a faild test is leaking past the injectors)
Injector test (12ohm reading across the terminals)  

the CPS can also cause a missfire without throwing a code...  

Yea! The CPS. Good thought!  

"started" pulling the CPS last night. Bottom bolt, not too bad. Top bolt, not so good so far, desperately trying not to strip it, soaking it in PB Blaster again.  Any good ideas about how to get a better shot at it?  Lying on my back until 1AM was, um, unpleasant.....  

New (reman) distributor, seems OK.  I'm going to remove and check the CPS first, then I'll try the fuel pressure test tonight if I can, followed by the injector test and then the leak down.  I've never done a leak down test before, so i'll have to figure that out.  

Sometimes you can tell without actually doing the leak down test. Hard starting when hot is an indication. Also, turn the key on, (pressurize), turn the key off. Wait 10 minutes, listen through the fuel filler neck, turn the key back on. How long does the pump run? One second is ok, but 4-5-6 seconds not ok.  

Sounds internal to me. i would do a compression test  

seriously, i just got done swapping motors in my 98 xj old motor had 210,000+ did kinda the same thing as you are describing before it spun a rod bearing for lack of oil pressure to the number 1 rod bearing come to find out the oil pressure sending unit was bad (i would strongly recommend testing or replacing it) compression test on old motor was terrible, also your throttle position sensor, o2 sensor, manifold absolute
pressure sensor can cause all sorts of weird codes come up. if they are bad. A chilton's book will tell you how to test different sensors and what to look for.  

yeah, I plan on doing a compression test this week.  Never done one before, but again have a friend that has and can help.  I'm still trying to get the dang bolt out to get the CPS out and take a look at it and/or replace it.

Oil pressure guage reads 40 at idle and anywhere from 60 to 80 under load, not sure what normal is on these engines.  

Click my user name for this post. You will see my e-mail address.

Send me an e-mail and I'll return it to you with files for the diagnostic and repair sections from the Factory Service Manual. Chilton is not very helpful by comparison!  

STRICTLY MY OPINION!!!
If the CPS sensor was giving you trouble, it would be all over the place, if it would run at all.
If you have access to a timing light, put it on the wire for cyl#4, or any other problem child and see if there are any "skips" in it.  If there is, then its an electrical problem. If not, then a compression test is an order. I would also check your wiring harnesses for corrosion.  A bad connection could cause an injector not to open.
** For sh!ts and giggles, try swapping around you spark plugs. I have had bad spark plugs from the factory before.. being a generator mechanic and doing many tune ups on v-16 motors.  This problem may not show up with the timing light.
Drop me a line if you have any questions @ benjorno@aol.com... always willing to help as much as I can.  

I agree it may very well be unrelated to the CPS, but I figured that taking it out and comparing the resistance to a new one wouldn't be a bad idea.  It just took me 2 days to get the dang top bolt out.

I like the timing light/skips idea and will add that to the list of tests.  I'm planning on checking the fuel pressure tonight after either reinstalling or replacing the CPS.  If it runs, I'll take it across town to borrow a timing light again and see if anything has changed.

Again, to you and all others keeping up and helping trouble shoot this:  THANKS!  

UPDATE:

I replaced the CPS, no difference.  I also decided to swap in stock Champion brand plugs and while at it make sure distibutor was set correctly.  Got it to TDC, reset distributor, replaced plugs, now it won't start.  It gets a spark to the plugs but won't start up.  No codes, nothing else.  The fuel rail does build some pressure (press the relief valve and it spits fuel).  I checked all connections and even checked to see if camshaft position sensor would generate current which it does.  Any ideas why it won't start?  

When you say TDC, are you sure it is on the compression and not the intake stroke?

Step 5,6,7 of distributor removal section in section 8d.

Ah, 8d...