My take in your quote after each section below, I hope it doesn't sound too blunt, but
every single one of the things I recommended I do with every single engine build and hydraulic rollers are by far the most common for me in both SBFs and FEs.
Thanks for your thoughts, I do appreciate the input. I'll try to answer your questions and concerns.
The method I use to adjust valves is to have the opposite number in the firing order to the one you're working on at full valve lift, then adjust the other one. So #1 at maximum lift, adjust #6; #3 at max lift, adjust #5; #7 at max lift, adjust #4, etc.
That seems like it might work, but that hurts my head

nobody needs to try to educate me why it might work, EOIC is easy and industry standard and not affected by cam design. As the exhaust valve starts to open, adjust the intake, as the intake valve starts to close, adjust the exhaust. It's easy and fast and works for every engine, and make sure you turn it the right direction
When degreeing the cam, it was found to yield a little less lift than the cam card indicated - .568" on the intake, and .580" on the exhaust, versus Lunati's .571"/.587" spec.
That makes sense, you lose a little than the strict ratio provides, especially if you didn't optimize the pivot height, but how about ICL, is it where you expected (not too advanced or retarded)
During engine mock-up, clay was used on the valve reliefs of the #5 piston. The FT springs were removed on that cylinder and replaced with lightweight checking springs. I did not have a SBF solid roller lifter, so a HR lifter was used, after pressurizing with oil. These valves were adjusted for zero lash + 1/2 turn, then the engine was rotated by hand through four complete revolutions. With no head gasket in place, the valve-to-piston clearance measured .078" on the intake, .083" on the exhaust. The Ford Racing head gaskets are .040" thick, so the actual clearance would then be .118" Int, .123" Exh. So valve to piston clearance should not have been an issue, as also evidenced by the 160 +/- compression specs.
Goofing around a bit, but again, hurting my head. You WILL have more with real springs, you SHOULD have more with the head gasket, but it may not be linear, and I am not sure you can truly tell you had seen the real lift with that method with the hyd roller. A single solid roller is cheap, I do not believe that your lifter setup could be guaranteed to be not compressing, nor can it be sure it didn't compress a little when it hit the clay. I will say I made a little inverted top hat that I use with hyd rollers and a pushrod length checker, it takes the plunger out of the picture, but I usually use a solid roller unless I can't get a pushrod length to work for checking, then I use the top hat
When the Flo Tek FT springs/retainers/keepers were removed, they were simply replaced with the Trick Flow parts. I did not have a height mic here so no measurement was taken. All of the HR lifters were pre-lubed prior to the initial valve adjustment, and no binding was felt as the engine was rotated by hand through numerous revolutions. So it was assumed...foolishly I see now...that we had the necessary clearance.
I do not believe it is a rocker or pushrod problem, ball/ball pushrods usually don't contact, a rocker trunion that style usually can rotate 360 degrees (if unbolted), and although Brent is right about the slot in the aluminum, it would have to be seriously wrong pushrod lengths and pivot point to have them smack that style, still worth checking though! Additionally, the rocker could be hitting the spring if too large of an OD, to check that, look at the bottom of the rockers toward the springs, they'll be chewed up. However, a spring height not measured is
almost always wrong in both pressure and height from what you want. In fact, after setting up too many heads, I haven't found springs that match each other in pressure or coil bind, or installed heights that match each other without shimming. High end heads are closer, but even those vary It really takes some thinking sometimes. It is very likely your spring and retainer combo doesn't match your heads and cam.
Amazon is supposed to be bringing me a height mic tomorrow, and we will begin a thorough check of what clearance is actually there. I concur that the exhausts may well be the culprit, but I doubt that the intakes are much better.
Given what you wrote here, I believe you had many things you need to look at even if you find installed height wrong tomorrow.
1 - Verify spring height, and it would be even better if you had someone check pressures and coil bind
2 - Once you verify or fix that, check clearance again with a solid lifter using EOIC on that one cylinder (there are other ways to cheat if you don't have one like my top hat, but given where you are, a single would be cheap to do, and at the same time look for the rocker hitting anywhere
3 - Reassemble and set preload by the EOIC method... EOIC is so much less thinking and not cam profile dependent. Your zero+1/2 is good, but be very careful where you determine zero is, and if any of the adjusters look different, check again, we all do that as a BS test.
In the end though, at any one step, if you do find something wrong, don't stop there, do the other things too. As I said it's not "some engines" guys like me and the other guys do this way, it's absolutely
all that we go through those steps.
Thanks for taking the time to spell it all out, the answer is there, just need to check everything (and on EDIT...get the right rocker studs for the mismatching ones)