Yes, the spring height measurement is not counting the 'cap' ( the retainer). What tool are you using for the measurement?
The issue is that the installed spring height looks to be abnormally short; that is valves, valves seats, retainers, keepers, & any shims. I'd be looking into what retainers and keepers you have first, or if the springs have shims under them. I've been looking at your pix in post #1... are the keepers protruding up out of the retainers? It sorta looks that way. I just wonder if some 10* degree keepers got put into some standard 7* retainers, or some other mismatch is there between the 2. That would tend to push the retainer down. Just thinking out loud....
You have a VooDoo cam with fairly quick ramps. The need for the heavier springs is driven by that. And the springs you have indeed have a pretty low coil bind height.... meaning you won't do a ton better. I don't have numbers in front of me, but I'd not expect the stock spring to be as good for coil bind height.
If I work through your numbers with the increased rocker ratio versus the cam tag, and try to account for lift loss due to pushrods angles, the exhausts looks to be getting in the range of maybe .040"-.060" from coil bind, and the intakes are a bit more. So getting on the verge of concern IMHO....
