I don't know the costs of a crate engine at your side of the pond, here it will not be a penny saver.
Love the unlimited options you guys have there.
Since the valve stems are evenly high, that cyl #3 push rod length will require exactly the same length as any other cyl. My guess is even after replacing that rocker shaft you will measure the same since the length is determined by lifter (height) and valve stem height only.
You are running .050" pre-load, reduction of .015" due to the shaft being out of round would still be covered within the pre-load tolerance.
I did not find any stroke length of those HT-967 lifters, since you are at .050", i think they would be somewhere in the middle of the range, right?
Other issue could be the retainer is bottoming out against the valve guide but this you also checked already. (valve guide height measured from surface is same?)
Springs and push rods solved the rattle on the other bank, this side still is hiding something but ramming a pushrod through a rocker is an indication of binding up in the bottom or the pre-load disappears and it hammers? Or oiling problems, but that seems out of the question since the rest are fine.