I had an issue with my '86 2.3, it was burning quite a bit of oil and the cat clogged. Could hardly get down the road. Fixing the cat restored the power.
The 2.3 certainly isn't a race engine but it should get out of its own way. If you have an infrared thermometer you can check cat inlet and outlet temps to see if the cat is dead. A muffler shop can check backpressure in the exhaust system.
You might want to do a compression check to see if you have cylinders low on compression. The Fours are notorious for burning exhaust valves when the valve adjustments are neglected. So that's a good thing to look at, too!
Regarding the swap, if the 2.6 is running well, not using oil or any other nasty habits, you may not need a rebuild. The bottom ends are quite stout and the only real issue down there are the crankshaft thrust washers. So be sure to check crankshaft free play (forward-to-aft) and if there's a lot, you should tear it down for inspection. You could also pull the oil pan when the engine is out and pop a few main and rod bearing caps to see what the crankshaft and bearings look like. Probably a good idea to reseal the oil pan anyway, it's one of those things that are almost impossible to fix once it's in the vehicle.
You'd probably be better off swapping the MUA5 tranny along with the 2.6, since it's a stronger transmission than the MSG. You'd also have to retrofit a hydraulic clutch master cylinder since the MSG uses a cable-operated clutch. But you've got a spare parts rig with all that stuff on it, Piece of Cake!
If you do decide to leave the MSG in place, you can mix-n-match the 2.3 and 2.6 clutch/flywheel parts to bolt up the 2.6. One of the 4-cyl swap Gurus can help with that, I can't recall which parts you'll need to use.
IMHO if the bottom end of the 2.6 checks out, I'd leave it alone. Especially if it's not burning oil. These are known to go 200-300K without big issues.
But do check out the thrust bearing, it is one known weakness of the bottom end.
Heads can warp/crack if overheated, valves burn, but at least a head can be replaced in the vehicle without too much trouble. Bottom ends are much harder to fix!
'90 3.4 Troop LS;
'89 Troop RS (Exhaust Valve Challenged), now gone to a Good Home!
Yes, I am a Trooper-Holic!!!
Keep On Troopin' !