I'm sort of jumping into this discussion without reading everything, but it sounds like the speculation is that you're getting noise because you over tightened some bolts that eliminated the required clearance with internal parts. My thought while reading some of the posts was what I think you're getting at here. If the grommets failed while being tightened they would allow more compression and you wouldn't be able to achieve the same torque with the expect cover clearance.
Maybe Chris is correct for what's causing the noise, but instead of it being an issue of over tightening the bolts is an issue of the grommets failing as they were tightened.
The “speculation” is from bgen. Until he mentioned it, I did not think it sounds like that issue.
To catch you up….
At about 200 miles on the break-in I was continuing to attempting to diagnose the sound – deeper than a rocker tick, more like a very light knock. BUT.. the input shaft seal on the tranny was leaking badly. The rear diff and the power steering gear box are both leaking.
So… I decided to stop and fix those and then get back to figuring out what the noise is.
I’ve been “listening” to engines and taught by my dad (who was a trained auto mechanic) about sounds and vibrations, since I was old enough to speak in sentences. After spending 1000s of dollars rebuilding this engine and then have a noise that doesn’t sound right makes me very unhappy. At this point, I cannot determine for sure what it is. I am very much hoping bgen is correct, and I somehow over-tightened the cover and inside top of the cover is contacting the rocker rack.
I may be overly analyzing this, but I don’t think so. I have several thoughts on what it might be and I have a short list of tests I will do when I can drive it.