Not much that will give you noticable hp gains on your 2.9.
I know you said that you didn't want to do an engine swap, but a 4.0 is near plug and play, and will give you a pretty good bang for your buck.
AJ
On an 87, swapping in a 4.0 requires a bit of wiring work. I wouldn't recommend it for someone not good with wiring unless they know someone who can help them with that side of things. If he had an 89, it would be a lot easier of a swap.
That said, short of rebuilding the engine and doing some major work, you're not going to get any huge performance gains out of the 2.9, so if you're after some big gains, an engine swap of some type is where it's at.
If you're just looking to do some odds and ends to make some improvements....
1) Ditch the EGR system. An 86 motor will have it if nobody removed it yet, but the 87 model year didn't require it. Chances are, it's probably not working right anymore either. If you're doing the exhaust, you might as well loose it.
2) Make sure you have the larger throttle body. If it is out of an 86, you should have it. A tennis ball should pretty much fit in the end of it if you have the larger one.
3) If you're ambitious, strip the motor down to the block (you can do it without taking the motor out of the truck). Grind the valves, port the heads and intakes (port matching/gasket matching only, don't worry about polish and all of that). New gaskets to seal everything up right.
4) While you have it apart, get a machine shop to convert the rocker arm assemblies into free-floating assemblies.
5) Replace some sensors. O2, intake air temp, manifold absolute pressure. While you're at it, put in a 180* thermostat to help reduce the chance of cracking the heads.
6) Headers and exhaust. I had my exhaust done by a local shop that does custom work. They ran 2-1/2 stainless all the way back on my choptop (4.0, you probably would be fine with 2-1/4). High-flow aftermarket cat and Flowmaster 10 series.