Finally opened the gauges this morning and set about adjusting the valves. I have no idea how out of spec they were. I had it in my mind that I was gonna adjust them no matter what, so I didn't even think to check them before backing off the lock nuts (stupid). Seems to be a bit quieter now.
The fuel injection conversion came with an FJ-60 style distributor. The cap on it has two vacuum hose type holes/ports on it. I ignored both of them. A couple of folks have told me that I needed to use them to properly vent the cap. A couple of Mud searches revealed that the larger port was supposed to run to a filter in the cabin (or 'high' up on the firewall) while the smaller port was supposed to be connected to a vacuum source. The idea being that the vacuum would constantly pull warm dry air through the cap. I picked up some hoses and a filter from the parts house and plumbed all this while messing around with the valves.
Also, the truck was idling around 1000-1100 RPM. I wanted to get it down to 700-800 but never got around to adjusting it. I rotated the distributor cap while in there today and got it down to 750 or so. The idle is quiet and smooth now. This might end up biting me in the ass, though, since it crawled without stalling at 1000 RPM...I kind of got used to not having to mess with the throttle on some trails. We'll see...
I had my idle set to the minimum, which I think was in the 700-750 range. No problems stalling. It will still try and maintain the idle.