Ok, thanks for the replies. At first, I didn't think it could just be hydraulic lash adjusters, but what you are saying seems probable. I went through everything again, removing the upper timing cover and checking the marks against the distributor rotor and the crank pulley marks. All looks perfect. I read a few posts about setting timing and figured out that it can't be 180 degrees off if the rotor is pointing at #1 and the marks are all correct. I started it again and she clattered on about 2 cylinders and smoothed out a little. I shut it off and tried again and it's down to 1 cylinder making noise I think. It definately isn't missing, but it's getting better, but taking its time doing so.
So it idled about 15 minutes like that last night, checking timing, and checking connections, and I ran it another 15 tonight reviewing timing, and it still clatters (sounds like maybe one or two HLA's).
I cleaned the pistons with some SeaFoam and a 3M scotch-brite scuff pad and it really cuts the gunk nicely, but leaves a slippey surface. I have used it previously in my SHO, cleaning the intake through the brake booster vacuum method with good results, but I wasn't sure about using it in the crankcase. Along with the head work I did an oil change, using Valvoline high milage synth blend 10W30. I could add the 3/4 can of sea foam and run it a bit but I'd have to read up on it. I don't remember how long you should try this.
Thoughts? I'm planning on buttoning up the splash shields and putting the wheel back on tomorrow and taking it for a short drive to see if it ever settles down.
Az, I hope I don't have to pull the head to pull those HLA's. This was a ton of work. Wonder if I should talk to the machine shop about it.