The fuel timing didn't look great (I'm very picky about details like these):

This issue is very common and it's apparent in at least half of VE TDIs. Optimizing the timing will restore power and possibly fuel economy.
An 5-9 PSI electric fuel lift pump was added last Saturday. As a result the fuel timing is noticeably improved.

It pulls harder in the upper RPM range now. Another common cause for poor timing is the collar walking out of the case relief valve (see middle valve in the picture below). The case relief valve is in the diesel fuel injection pump:

The collar can be pressed back in, but it'll walk out again especially if more power is in the picture. To prevent this from happening, I will do the
keystone mod:

The above picture is a homemade keystone courtesy of
StealthTDI. I will be using a different design made of steel.
I'll post the updated timing graph after it's done.
The following mods were also done last Saturday:
- Euro 0.216mm injectors
- Hammer mod (injection pump calibration). Originally 0.8 IQ, now 3.2 IQ.
- Stage 1.5 ECU tune
Boost looks good and I haven't done any tweaking yet. Leaving it at just shy of 18 PSI sustained for now (typical max. safe boost for a stock K03 turbo):

I would probably estimate it at 190ft-lb torque right now. When I had stock injectors and a Stage 1 tune, a MK3 VR6 buddy commented that it pulls like a VR6. But there is much more potential as it's currently running a mild tune and the K03/K04 hybrid turbo is designed for 22 PSI. I am happy with the way it performs now, though.
Maybe I'm spoiled by my old 2006 MK5 Jetta TDI (now my wife's), but the AHU vibration at idle is a bit much. It's smooth as glass once the RPM is >1100. I need to ensure that I have stock TDI mounts installed. If not, time to order some.