Might be worth having the valve job redone by a machine shop that can get all of the intake seats the same and all of the exhaust the same. There will still be a difference between the two in height but by then it should be like .020 or less between intake and exhaust.
Other option is cut stems to equalize intake stem heights on each head then exhaust to try and end up in the spread or separate lengths per int/exh instead of 3 and a bunch of varied preloads/lifts.
Another option...5.011 vs 5.025...other words..+.050 vs +.100, .150,.200
Play with valves and cutting stems. If one was equip to do so.. could be attacked a few ways. Since we know the seat depths are all over the place but in a bad way..
how are the spring heights?
Sounds like shims or locks or both. I just used -.050 locks and .060 shims to bring in the height needed...