I will try to help
1. Which manifold, the exhaust or intake I can go take a look at mine as it is all stock right now, but if it is the one on the exhaust for EGR I took mine and just cut it and welded the end shut, you may be able to find a metric pipe cap that will fit in there.

2. Could be due to a couple things, 1. your drum could be warped (Believe it or not they actually can warp) or 2. Your load proportioning valve is stuck.

3. As far as i know on older vehicles the only way to kill the high idle is to tap the gas after about 5 minutes.

4. Is you PCV valve stuck, it may be holding crankcase pressure, and when you rev it the seals cant hold the oil in (Could have something to do with your first question).

5. If your clutch was going I would think it would be easier to put it into gear, if you understand the basics of how a clutch works, i would think that your clutch cable needs to be tightened, or if you put floor mats in it could possibly be restricting the travel of the pedal and causing it to not fully disengage the clutch.