Ok, finally have had a lot of seat time in this Golf after countless problems.
First of all, it's back to running an N/A pump for the time being until 10 years from now when I can afford a Giles pump.
Some more background info:
NA block, solid lifter head
Engine rebuilt, used thickest MLS head gasket to lower CR a little. Pistons are Swaintech coated.
Head had a valve job, and is mildly ported, intake ports are D-shaped now.
Back to running a stock VW TD T3 and exhaust manifold
TDI intake manifold, mildly ported lowers.
No intercooler right now.
I don't know where it is timed, I guessed.
Overall the car runs pretty well. Starts INSTANTLY, hot or cold, now that I have new glow plugs. I usually use the cold start lever for about 5 minutes, seems to be smoother that way. Good power when driving normally, though I basically don't get any boost at all until I rev the piss out of it. That is, normal traffic acceleration to 35 MPH shifting normally, there is no boost. I can hear the turbo starting to spool but nothing on the gauge.
I have the pump turned up a bit, there is some smoke off-idle until a little higher in the RPM's, but not much. Using light pedal, there is no visible smoke from the rear-view.
Driving at 55-65 mph, (guessing since the speedo does not work) EGT's go up pretty high, will hover around 750 but even a slight increase in throttle pedal for a hill or something and they shoot up to 1100-1200 pretty easily. No smoke and no boost during this time. Unless I am going very fast, like probably 75 mph or so, there is no boost in 5th gear even with the pedal floored. Driving on the highway at those speeds, EGT's are usually 950 at the least, sometimes going to 1350 or so if I have to speed up a little but usually they hang around 1100.
If I try to accelerate hard from a stop, I'll get maybe 10 psi in 2nd-3rd-4th. EGT's usually don't go very high when doing this, maybe 1100, and there is no smoke except for a little between shifts when I get back on the throttle. But spool is VERY late. If I had to guess, I would say 3000 RPM's or so before you see anything.
Now, when I had the TD pump on it, it would hit about 18 psi or so and I could hear the wastegate opening, so I know it's not stuck open. EGT's were still pretty high, and the boost still was very late coming on, but it did come on a little sooner and climbed faster. There was some smoke though.
I know the NA pump is holding it back some, but if there is enough fuel to smoke a bit off-boost, there should be enough fuel to spool the damn turbo. Plus, EGT's seem way too high to me when I'm barely using any throttle to keep up at 55-65 mph.
The car does feel pretty slow, fast enough to merge on to the highway without worrying about getting run over, drives through town really nice but not very quick. Off-boost power in the lower RPM's seems pretty good. Better than my Audi even.

Anybody have any ideas what's going on? Could it be a timing issue? How does timing affect boost and EGT?
Thanks in advance-
Brendan