I'll finish buttoning up a TB job on my 2000 Jetta today (soon to be my son's beater). It has almost 370k on the odie ... cannot imagine replacing the head gasket, front crank seal, rear main seal, etc., as they are showing no signs of leaking!
OP, if you remove the Intake Manifold for cleaning, cleaning the intake ports in the head is highly recommended. You just need to make sure that the valve is closed on the port you are working on. Scrape, pick, gouge, vacuum, and compressed air blow-out, repeat as necessary (can be a very messy job).
You do not want to re-install the Intake with the head intake ports looking like this:
Which could (in this case did) result in this......... (also notice the Intake valve to the right)
When you remove the Intake Manifold, the crud crust from the runners to the ports in the head is broken. That junk can and will break loose and be ingested by the engine. If you are lucky, it will pass without incident!