Cylinder Head CCs & Comp Ratio; Need Help!

I just took my HO 4.0 head to the machine shop for rebuilding. I ported and polished the head myself and found articles on how to CC a combustion chamber, so I checked all 6 chambers before it went to the machine shop and measured ~ 56ccs. I told them to mill off .015" so I could increase my compression. I was trying to get my CCs down to about 53-54 ccs. Well, the head came back and the chambers are now 57-58 ccs. I called the shop back this morning and had the manager ask the machinist who worked on it how much he took off and he insists it was .015" as instructed. The shop is well respected for their quality. What's going on? Could the valve job sink the valves that much? They did have to replace 2 valves (1 int, 1 exh; because I ruined them while porting) and the chambers with the new valves are measuring around 56.5-57ccs and they do appear thicker than the old valves.

I'm tempted to replace all the valves and mill an additional .010" off. Should I have them mill more off the head? Will this cause problems with the pushrod length? I don't know how forgiving the hyd lifters will be. I'm already using the MP head gasket (.042"). I am also using the Comp Cam 68-232-4 cam and lifter set.

Thanks in advance!!

Don't mill any more off the head. It should be perfectly flat now so leave it, otherwise you WILL run into valvetrain geometry issues and need to shim the rocker arm bridges to correct it. If the chambers are indeed 56.5cc after milling, combined with the MP head gasket, the CR will come to ~9.0:1.
It's just possible that the combustion chambers might have been enlarged by the porting/polishing process.

I measured the chambers after all the porting/polishing was done, so I know that the increase either came from the valve job or my cc'ing methods. I've tried measuring the same chamber 2-3 times and I seem to be getting repeatability, but maybe I am doing something different from before the head was machined. I think I'll try buying some better equipment for CC'ing and/or replacing all the valves with new ones. I really want to get all 6 chambers the same (right now they vary up to 1.5 ccs from each other).

I've never seen the 4.0's combustion chamber but I think it would be pretty noticable if the valves were sunk deep enough from the valve job to increase the volume of the head 1-2 CC's after the 0.015" was taken off. And if the valves are sunk that deep then you're hurting flow anyway. I measure combustion chambers at work all thime on motorcycles and it's never a bad idea to have someone else measure the volume just to make sure.