Sounds like a good journey youve been on!
I wonder what temperature the charge air at the inlet manifold measures at with stock configuration, simple larger air-to-air IC or water-to-air IC?
IME a "rattly" 300tdi comes down to:
1/ tappets and top end issues : including adjustment, lash caps, rockers, rods etc.
2/ injectors
If tappets and top end is tidy and If your injectors have 320 on em, might be worth a change out?
Oh, and by the way, welcome! and killer forst post 
Steve
'95 130 dual cab fender (gone to a better universe)
'10 130 dual cab fender (getting to know it's neurons)
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