Sorry so late to this thread but...
Dump the Performer intake. It's peanut port and will cause a significant restriction. L29 heads are LARGE OVAL, just like the old 781, 049, etc. and you can easily see this when you line 'em up with a gasket.
You've already found out that the rocker stud bosses are tapped, but the section that threads into the head is a good bit smaller than conventional. Comp cams has studs that will work.
The L29's valvetrain is non-adjustable or net-lash as opposed to what we're used to (these are very similar to LS valvetrain setups). Once you get rid of the Gen 6 rockers and replace them with adjustable type, you can set valve lash at zero plus 1/2 or 3/4 turn just like you're used to. I've always had to replace pushrods, OEM are too short.
All Gen 6 heads will work on Mark IV blocks, just remember to get the gasket that's correct for the BLOCK.
I've worked on several of these and keep in mind that these were developed for clean emissions, requiring much less timing that conventional open chambered heads, and torque. You should have a noticeable seat-of-the-pants feeling with these installed. If you don't, double check valve lash.
Glad you learned about chasing threads...more people blame poor block material for pulled threads than their lack of preparation in cleaning the threads.
There are several threads on these heads at
www.teamchevelle.com and you'll find a good bit of info there. One thing for sure. you're probably not going to grind through them when trying to port 'em, they're plenty thick. There is at least one thread at the Chevelles site that has pics of one that's been cut up.
And OP: next time you have to work on a big block in the truck, use a cherry picker for lifting and lowering the heads. It sounds like overkill but I promise your back and hands will thank you. I use rocker studs to get it at pretty close to the right angle when it's hanging.