Growl and minor loss of power

I have a 2002 Jetta TDI auto that is confusing me. I recently ran a tank of biodiesel through it from a filling station in Berkeley (first bio diesel I ever ran), and by the time I was at the bottom of the tank it had started to run poorly. I also have a minor growl under the hood that tracks with engine speed. The car has to be under load to hear the growl, and the power loss is only in the range of 20%.
I have the engine apart now, and didn't get around to recording the sound before I did so. The growl becomes very noticeable around 2000 rpm, and the turbo seems to lag until 2300 rpm. It boosts slightly, but I can feel it really start to come on after 2300 rpm or so.

I don't know if the biodiesel caused an issue, if a pulley is going out, turbo... I did spend a few hours of very spirited driving last week, but it ran fine afterwards. I pulled the intake manifold off and cleaned it, but it wasn't in bad shape. The fuel filter has about 15k on it, the intake is clean, oil is only a few thousand miles old (Mobil 1 diesel truck formula). New trans about 40k ago.

Any ideas? Anything I can do to check the turbo while I have the intake off?

I can't tell if any codes have been thrown because my check engine light comes on due to a failing glow plug harness.

Thanks,
Camelman

I forgot to mention. I checked the vacuum hoses around the intake manifold, and they all held vacuum. I plan to replace some of them anyway since they are getting old. Can I just use regular vacuum line from Kragen/Autozone/Pepboys, etc?

Just ran across this post. http://forums.tdiclub.com/showthread.php?t=107803&highlight=fuel+temp

My valve was completely apart, but all the parts were still in the hole. I reassembled them, and will restart the engine as soon as I get it back together. The fuel pump was VERY loud recently, so hopefully this was the issue.

Camelman

Update on the fuel pump valve rebuild. I put the cleaned intake back on (it wasn't very dirty even with 70k on it since the last cleaning, and took it for a drive. It runs like a top again. I was losing power and getting poor turbo response with that valve apart. Once it was back together the turbo kicked in like normal, the pump got quieter, and the engine runs as smoothly as when I bought it.

I love my car.

Camelman