First, hi. I'm a noob to IDI VW diesels, but not gasser VW's. We picked up this '84 Jetta Diesel a little over a month ago and I've been working on it since.
Before:

After:

Anyway, on to my question. Since I'm new to these, I need a little guidance in figuring out an issue we're having. I have a slight hesitation/stutter/stumble just off idle. Also have an issue where coming from cruising to idle, it idles fine for a few seconds, then drops what feels/sounds like a couple hundred rpm, and it will occasionally, slowly, go up and down that couple hundred. I also get a LOT of black/dark-gray smoke at almost anything over 1/3 throttle. The first tank I just figured it was the old fuel. But now I'm on clean fuel.
Some info:
1.6 n/a 5 speed
new fuel
new fuel filter (changed 150 miles after filling tank with new fuel)
new oil and oil filter
new air filter
temps run right at the middle
lower crank case vent blocked (used to go to diaphragm pump, not have rotary style vacuum pump)
upper crank case vent is stock (into intake)
Mileage with old fuel - 40mpg
Mileage with new fuel - don't know yet, but it seems to be a LOT better. Went 150 miles and it's still touching the full line.
I have noticed very small foam-like bubbles in the line from the filter to the IP. Just figured this was normal
Symptoms:
Hard to start (long cranking and/or have to press accelerator)
lots of black/dark gray smoke above 1/3 throttle
somewhat erratic idle
hesitation when coming off idle, about 800 rpm above idle if I had to guess. Maybe lower. Runs fine otherwise.
very small foam-like bubbles in the line from the filter to the IP
Slow acceleration... wait, nevermind

If I think of more, I'll add it.
So, does this sound like I need to break down and buy the timing tools, or can should be checking elsewhere?