When you are checking your geometry and clearances are you doing it with solid lifters installed? If you are doing this with hydraulic lifters you are not actually seeing what max lift looks like as the lifters collapse some with no oil pressure.
And the bad thing about lifters is the contact area where the pushrod ball seats is a different dimension to the top of the lifter between hydraulic and solids. That's why they take different length pushrods. I would be tempted to check into some beehive springs. That would end your problems as long as they spec close to the springs you are using. tmm