My 1991 Jeep Cherokee 4L straight 6 started leaving a few drops of oil on the driveway at 150,000 miles. At first it appeared to be a rear main leak. When I investigated it was a timing chain cover leak blowing back to the rear. Not simple but within my old school capabilities. Since I had gone that far I installed a new TRW gear and chain assembly. The Jeep went another 50,000 miles with no problems.
OP: I agree you should check for cat restriction. In addition to explaining the loss of power, it could be why your exhaust manifold gasket is failing!
As to removing the manifold, yes it is a PITA that requires you to disconnect the intake manifold too, as it is a non-crossflow engine. There are 16 bolts, and the bottom ones are almost impossible to see or get to.
Also, which cylinder(s) are the ones with the compression issues? You might have a head gasket problem.
The 94 Ford 4.9L engine has an upper plenum that is somewhat easily removed to get at the valve cover gasket that is almost certainly the source of the oil leak. And burned valves from exhaust leaks are very rare on street legal automotive engines. High performance engines, especially aircraft engines might need special attention to prevent such problems but a For truck engine is awfully under stressed.
You need to do a compression test before you attempt a tune up. If you have low compression, the head has to come off for any fix, Just remove the exhaust pipe from the manifold. then take off the manifold from the head on you workbench. Much easier.
I would not mess with the manifolds, I think you are looking in the wrong place. I agree that the leak is probably the valve cover and that the loss of power could be the cat. But first, how is the idle, is it smooth? If the idle is smooth, then that would reduce the odds that you have an ignition problem or any valve damage.
You may have low compression, but while the valve cover is off, rotate the engine by hand, stopping at each point where a valve is fully depressed and measure how much that valve is open. Just measure the distance from the tip of the rocker to the head surface. If you have a valve that is not opening completely, it could be from a collapsed lifter, a rocker nut that has backed off or a flat cam lobe. Check for the rocker nut first.
After you have replaced the valve cover gasket, then do a compression test, if it is good, remove the cat and inspect it. Usually a blocked cat is caused when the honeycomb melts at the leading edge. You can see this by looking in.
If your cat is built into the exhaust manifold, you may have to just replace the manifold with a new one.
I tend to avoid taking off exhaust manifolds like the plague. The smaller ones are not as bad but the larger ones always seem to be under some spring tension once the engine is a bit long in the tooth. Once you take that first bolt out, the tension is relieved and it shrinks. Then it’s a bear to stretch it back into position…
TwinTurbo is right about exhaust manifolds changing their shape. I swapped out a 350 Chevrolet short block that had been badly overheated and sent the heads out to the machine shop.
During reassembly I found that neither one of the exhaust manifolds would bolt up to the heads again.The manifolds had curled up a bit much like closing a thumb and forefinger together and from one end to the other the holes were now about 1/4" closer than when removed. Quite a bit for a lowly 350.
So, call to the boneyard for a pair of manifolds… 
This tool wasn’t helpful for reinstallation of that manifold?
A tool is available to press small block Chevy exhaust manifolds back into position for reassembly.
The OP’s Ford 4.9L has 2 exhaust manifolds. The front and rear cylinders have seperate quasi headers and they usually don’t warp enough to cause a problem when reinstalling. The older carbureted version of that engine had a single exhaust manifold that was attached to the intake at a “stove” and when removed and seperated the exhaust manifold would often twist and become difficult to reassemble.
The symptoms mentioned by the OP don’t indicate a missfire which would be occuring if there were a significant loss of compression.
Update: I had a known mani leak and after getting in there, see that the valve cover gasket is leaking onto the mani crack (not sure if the leak caused the crack or vice versa). I replaced plugs, wires, cap, rotor, button and pcv valve to no avail but still working on that %& o2 sensor (it stripped even after using liquid wrench. So, out come the vice grips).
My suspicion is oil leaked into the exhaust fouling up the o2 sensor (fingers crossed). I got a mani from a bone yard and plan to put it on but want to be sure it’s the problem before doing all that.
Before you start removing manifolds, I would try tightening them. These engines are famous for vacuum leaks and a rough idle caused by lose bolts…As for the oil leaks, try snugging down the valve cover a little and see if that improves things…
Update: Finally done wrestling out that o2 sensor. Installing the new one in the morning. That WAS NOT fun!
Did the female threads in the exhaust manifold strip out?
No, it came out clean (Lucky me). That’s the old one on the right. The new one on the left’s going in tomorrow.
Update: I put in the o2 sensor and patched the mani leak w/JB Weld for now. I fired her up and immediately noticed smoke pouring out of the fIange just below the plugged crack! Now, I remember noticing the tailpipe shaking a lot lately and looked to find it’s rubber mount is broken (Probably losening the connection).
I’ve been soaking the flange bolts w/PB Blast and will try to snug them up in the morning…
Update: Operation snug up was a disaster. It didn’t budge. I ended up removing the fIange w/hopes of replacing the bolts but only 1 came out cleanly. Only the nut came off the other, stud still in place. I’ll try it only once more after soaking overnight in PB Blaster (scared of breaking it off).
Qusetion: I didn’t see any kind of gasket. Should there be one?
Update: FIange now tight. Now,only a minute exhaust trickle coming from the JB welded manni patch. Idling is perfect but still running rough when driven. I’m now thinking burning oil may have ruined the cat.
I’ll check for vac leaks 1st but can I just cut out a bad cat if I don’t need emissions?
I would have somebody do a backpressure test before condemning the cat
Perhaps it’s not even plugged
Might have another problem
Just for future reference, so you don’t end up more frustrated than necessary- if I plan to replace an O2 sensor, I just cut off the wire pigtail w/connector and use a deep well 6 pt on the sensor with a breaker bar to remove it.
Using vise grips sends shivers up my spine. They have their purpose but are not well suited to such tasks. A small pipe wrench is far better if you must resort to such things (didn’t use socket so bunged up flats). A pipe wrench gets tighter the harder you push on it. If you have room for vise grips, you have room for a pipe wrench…
Those flange studs are always problematic. They rust away in the exposed area and often twist off. If you take out the manifold, most shops can replace them for you fairly cheaply if you leave them alone. Once you bugger it up, it’s harder and costs more to fix.