Hi, you should have a minimum of .062 between spring coils at maximum valve lift. If you’re running .540 lift (assuming that’s the high side). You’re likely running a hydraulic roller Cam, opposed to Solid Roller, or the Pushrods would likely bend during initial lash settings- as there’s no oil pressure to pump them up to give you full valve lift.
The Springs, Retainers, locks should be matched for the specific Cam you’re running. Not only for lift, but you want to have enough seated spring pressure & adequate pressure to shut the valves @ High RPM’s, and know when Valve Float occurs. Are you certain there’s no slight Piston to Valve interference, and are the intake Pushrods bending & not exhaust or is it both?
If you’re running GT40/P Heads, this is a common issue, and I’ve repaired many that run E303 Cams with the GT40 Springs, some run 1.6 Ratio Rockers, others 1.7, (.498 lift, .527 lift). Max lift for those stock Springs is around .475 lift. Some bend Pushrods, some spare Pushrods & absorb it in the hydraulic Lifters and walk the valves, destroying guides, Valve Seals, and sometimes- Rockers.
When I build a new hydraulic roller top end, I have one Lifter i’d brazed so it’s at full lift, when I’m verifying spring Coil distance. Improper Valvetrain geometry can also bend Pushrods. Anything but VERY mild Cam setups I use Screw in Studs, Pedestal Mount is really not good for much else.
If you have not found your issue, as I’d realized this thread is over a month old, add to the thread & i’ll be happy to help, as well as others.
Hope you did find your issue. J