First of all, I am here to help those running a stock or mostly stock 2.5. I have no intent for this thread to turn into an ego/pissing match about how to build an engine. I have read nearly every page on this forum and found nearly everyone asking the same question (how to get more from your squirrels), and the only "real answers" seem to be to mod the crap out of it $$$$$$$$$$ or go V8. I am here to give witness to an alternative.
I started my 2.5 build several years ago and found a few things along the way that I thought I would share. I have stuck with OEM internal components in my build to see if more power can be made if modded in the right area.
My current setup is: 1984 2.5, stock/OEM crank/rods/pistons/cam/valves. I am running a late model long runner MPI intake with an adapter to run a Weber 32\36. I am running a home-made tri-y header that feeds a 2.25" Flowmaster, though I suspect a 2" would net better low-end power on a mostly-stock engine. For the ignition system, I am running a Summit Racing digital ignition box with an adjustable rev limiter. Rev limiter is currently set at 6k rpm. I decked the block for a sub-0.030" squish clearance, and have to run premium fuel. This engine flat-out pulls harder than any other 2.5 I have run with, and have even beaten several 4.0's in the mud boggs.
I believe the Jeep 2.5 and 4.0 heads both suffer from ports that are too large (for stock displacement that stays under 6k rpm) and poorly shaped. I have been successfully running epoxy-filled intake ports for several years now, and the effects have been VERY good. In my search for more power (on many different engines), I have found that port velocity has a very profound effect on overall power of an engine. I would NOT advise that you remove much material at all if porting this head. What keyed me into this was a question from my engine builder when I handed him the head early in my build (before I tried epoxy), "Those ports are pretty big! You spinning this thing over 7k rpm?" For reference, this guy has been building SBC race engines for over 30 years now. I replied, "I didnt change the ports, only sanded the rough castings smooth". So, here are a few things I have found to help this:
1) Advance cam timing. I used a Mr. Gasket#720-988G 4 degree key on my crank, available at many parts stores dirt cheap.
2) Good multi-angle valve job. The stock valve lift is a major restriction. A good valve job will increase flow at lower lifts.
3) Better cam with more lift: Clay Smith still lists cams for this engine
http://www.claysmithcams.com/hydraulic-flat-tappet/4) Not so inexpensive: Roller rockers. Others have found that the stock stamped ones flex, at the cost of lift. I would stick with 1.6 ratio as I suspect the 1.7's put too much strain on the 5\16 rocker bolts. Best price I have found is on the Harland Sharp S40196. I hear you can buy them in pairs from HS.
5) Last, but not least: epoxy. You would be absolutely amazed at how much better this engine runs with less than $30 in epoxy put in just the right places.
If sticking with the stock cam, I would recommend the 4-degree offset key and roller rockers. If you go with a good aftermarket cam, no need for the offset key as the advance is most likely built into the cam (check specs to be sure. If the LSA and centerline are not identical, the difference is the advance).
I have also found that the stock valve springs are inadequate, for an engine that runs past 5k rpm, even with the stock cam. I experienced valve float, which nearly dropped a valve in my engine. Luckily for me, the keeper ring land shifted just enough to cause a ticking sound that sent me looking for trouble. I upgraded to hardened keepers (Howards Cams locks pn HRS-93020 ) and two sets of springs (actually listed for a V8) from Comp Cams pn CCA-901-16. These springs are 353 lbs/in spring rate with a seat pressure of 101 lbs at stock 1.65" installed height.
I have also experimented with bumping the compression ratio, more in an effort to get a tight squish clearance than anything else. I have found:
1) The factory squish clearance (piston to head) appears to be in the 0.100" range (depending on head gasket). Completely and totally ineffective. Even if you were to get a hold of a 0.020" metal shim gasket and use the 4.0 pistons with taller compression height (Silvo-light 3242HC), you wont get it under 0.040", where squish actually becomes effective. You have to deck the block.
2) FWIW, the guy at Clifford stated they take 0.060" off the head to make a smaller combustion chamber, and don't even worry about squish clearance.
3) The thickest head gasket is Victor Reinz, followed by Felpro. I cant quite remember the specs, but I believe the Victor gasket was around 0.070" and Felpro around 0.063" compressed. I also found a 0.020" metal shim head gasket on my spare 1986 engine when I took it apart, but cant seem to find a listing for it. I believe this is the stock gasket that came on it.
4) Decking the block to achieve a 0.040" squish clearance seems to be the sweet spot that nets a good squish clearance benefit, but is right on the edge of pinging on 87 octane/stock cam/stock pistons. If you use the Silvo-light piston 3242HC, it has a deeper dish which should allow for a slightly tighter squish/higher compression ratio. Different cam timing will also effect octane tolerance.
5) On a tight engine, you cannot go below 0.026" squish clearance without risking contact with the head.
My quest for a tight squish clearance also led me down the path of finding more conservative ignition timing. Not much to note here except that the stock Jeep I6 distributor advance weights and springs are considerably more conservative in timing than the stock 2.5l ones.
Last, but not least: for anyone concerned, the piston to valve clearance on these engines is HUGE with the stock dished piston. I dont see a piston ever hitting the valve unless the valve drops from retainer/keeper failure.
Hope this helps some of you. Sorry, I don't have any real-world experience with larger throttle bodies on this engine, mine is carbureted.