This past weekend I finished putting everything back together.
I deleted the throttle body heater plates and the unnecessary lines beneath the intake. I used shorter TB studs and tried to run the lines to look as stock as possible from a quick glance. While I had my intake off I cleaned it out and gave the upper intake manifold a light coat of VHT high temp aluminum paint. I bought some 4-hole injectors and had them refurbished at Witchhunter.com. To plug the coolant ports I just used the old hose cut off and plugged with a bolt, silicone and a hose clamp.
edit: I forgot to mention that while I had the radiator out I flushed out a few handfuls of gravel that had made its way into my tank! I also blew out all the shit stuck in between the fins. The bleeder screw hole had been filled in with silicone, so I replaced the screw with an aftermarket one made of brass. Only problem I can see with it is that it may be easier to strip the plastic threads on the radiator, especially when the screw has been heated up by the coolant.
Here is a shot of the engine bay the way it looked when I first got it. This is before I had done any work:

The plugged coolant ports:
I'm a little worried about the air bubble that will be trapped in the coolant pipe - but I don't know how it would ever escape into the system to cause problems so I think its ok.

The vacuum lines from the valve cover to the throttle body:
I used a "crankcase vent hose" from O'reillys. It came in a little box for $2.99. It was 5/8 inner diameter but was kind of stiff and would fold at a sharp bend, so I used one of the original 90* elbows. I used a 180* junction to connect it to the stock hose coming off the valve cover.

The vacuum line to the Idle Control Valve:
Same crankcase hose from O'reillys. 90* bend off the stock lower ICV hose, one 180* junction in the middle.

Refurbished injectors:
I bought these Bosch 1280150556 injectors from dbgrubbs. I sent them the Witchhunter.com to be cleaned, refurbished and tested. They did a nice job but its expensive. I'm glad I did it though since the before/after test results showed a nice improvement. They replaced the filters, o-rings and caps - also a multi-step cleaning process.

And here's how it looks today, all put back together and clean:

Fired up and runs a lot smoother than before. I won't be giving it a
proper road test though until I check out a couple more things. I'll be checking on the timing chain/sprockets as well as dropping the oil pan to have a look around. I'm pretty sure they both have issues since there are noises coming from the top and bottom end.