Did you replace the rocker assembly? I believe the rocker piers are shorter in the later models, could be an issue. If the valve seats were ground excessively it could cause your problem. If the shop ground the valve stems too much it'll cause the same issue. So many things it could be, looks like you need to dissemble things and do some measurements and compare to factory specs. Won't be anything below the head at least. I would suggest NOT using shims or washers to adjust the pier height.
Also, the cam could have been ground with the wrong base circle. Regrounds typically have smaller base circle which would cause the reverse of your problem. Welded and ground or new billet can cause the issue.
Cam timing can be a problem. If the cam is off a tooth or two and you try adjusting by the timing marks on the harmonic balancer, TDC, you'll be off the base circle of the cam.
And one more, similar to cam timing. If the ring, the part that has the timing marks on the balancer, has slipped, your cam timing could be right but TDC can be off. Setting the timing marks at TDC with a slipped balancer would put your cam off closing up the gap.
