Last question first, and I'm sure someone will have a differing opinion, but for such things my go-to is
https://www.amazon.com/Super-Lube-92003-Lubricating-Translucent/dp/B0081JE0OO/ref=pd_sim_328_2?_encoding=UTF8&pd_rd_i=B0081JE0OO&pd_rd_r=S0EKCCKD85NXS0XRT5MM&pd_rd_w=1S5OX&pd_rd_wg=juL47&psc=1&refRID=S0EKCCKD85NXS0XRT5MM.
If I don't have that option, I've been known to use lithium grease or even petroleum jelly in an extreme pinch.
I would definitely check with GDE before going forward. I suspect they might want the code to be cleared first, so there's no causal confusion.
I have to admit you had me back-reading with that wastegate mention.
Your 2006 should have Variable Geometry Technology rather than a wastegate.
Also at idle, the boost should be no where close to 30-35psig.
If fact, if stock, I think it shouldn't go much over 22-23 at full throttle and maximum torque. (and I welcome all the experts to correct me if this is wrong) and unless programmed to ignore the condition, it should be showing an overboost condition if it's at 30-35psig.
Regarding the timing belt, I reassembled the belt and triple checked that everything was properly torqued that was supposed to be.
Then when all timing pins were out, turned it over by hand at least a dozen times with the injectors out to make sure there wasn't any binding.
Then installed the injectors but left them unplugged, and cranked it over for a few 10 second runs, to check that compression was even, and no obvious external leaks (injectors and glow plugs), and that the oil pressure was good.
Only after all that, then I proceeded to fire it up, but (because of the wiring problem) It wouldn't run as long as the You Tube videos, but it was enough to let me know all was well timing-wise, so then I proceeded to put the timing belt cover on, etc.
RE thermostat: Mine not only had a bit of a rattle, when it was installed, if I leaned over the engine with my hand on the outlet, there was an obvious movement of the crimped on top as the o-ring inside was compressed. When I noticed, I quit doing that.
Whether it's normal or not, I don't know.
For cleaning out my intercooler, I cleaned it out of the vehicle, front facing down, and over the course of a month, went through roughly a quart of Dawn Heavy Duty Degreaser, and over 4 gallons of Super Clean. (plus a small swimming pool worth of water)
I also used 2 T-handle clam guns, and a couple of pickup inner tubes to alternate pressure and vacuum on the inlet and outlet to make a kind of washing machine effect.
The only ultrasonic cleaners around were at Radiator shops, and there was no way they were going to allow that thing in their tanks, since it had been completely filled with what was once Motor Oil.
I stopped when it sat full in the sun for a day without having an oil-slick at the water's surface.
Once clean, though, they were happy to charge me $20 to pressure test it, and put that special black radiator paint all over it.