I can completely sympathize with you right now. I made the decision to have Livernois build and tune my engine a couple years ago based on this "reputation" also. In addition, I only wanted one shop doing the work so if something went wrong I knew who to hold accountable. The build took way longer than originally quoted. Hold up was the new head castings, core shift, etc. Dan Millen personally told me the new castings and CNC program were going to be worth the wait so that is what I did.
Finally got the car finished and back. Immediately I knew there was a problem. Big oil loss and blue puffs at start up. Livernois encouraged me to drive the car for the season and they would fix it over the winter. While they were "fixing" it I went to the shop to inspect the work. I didn't get to see the cylinder heads for whatever reason but I did ask to look at the cams. Good thing I did because they had been damaged on the mechanics cart (as it was explained to me).
Again after a long wait I got the car back. I was told the same story about the valve guide problem with their supplier and it was now corrected. I put a few miles on it and went to drop a borescope into the combustion chamber through the spark plug. Went to remove the spark plugs and the socket was the wrong size. Changed sockets, pulled the plug and found Livernois had swapped my highly touted new castings back for the old with out ever discussing this with me which in the end has now cost me more time and money.
Didn't really drive the car this summer because the thing just gets too hot. It drove better and more consistent before building the engine. To address the heat, this winter I took the blower off. While off, I peaked down into the intake ports. All looked good but the very last intake valve in the number 8. I was also surprised by the impressions left around the intake port by the OEM o-ring. The intake port had been CNC'd so long it was cutting into the cross section of the o-ring leaving a stepped transition and half the cross section of the o-ring to try and make a seal.
I mic'd the intake ports and OEM o-rings trying to make sure I got as straight as possible across but there may be a little variance. What I saw was th long end of the intake port measured 2.655" with the short being 1.164". The measurements I got on the inner diameter of the OEM o-ring were 2.654" (L) x 1.489" (W) with a cross section of .0575". Again these might be off by a couple thousands here or there but should be pretty accurate. At my request, another engine builder/performance shop, who has had problems with Livernois heads and now uses RGR, measured the intake ports on a set of RGR heads for me. They came out 2.5xx" (L) X 1.2xx" (W) (sorry I couldnt find the email with the numbers to be more exact).
Off to Livernois again to discuss this issue and they conveniently have a set of StageIII heads on display. Pulled out my micrometer while waiting and the length of the port was 2.5xx". I ended up speaking with Andy Ricketts who thought the oil might be due to a poor spray pattern from one of the injectors. We placed the injectors on the flow bench and nothing really stood out but one injector had a suspect pattern. While there Dan Millen also threw out the idea that there might be a leak around the manifold on that cyclinder. (With only half the o-ring trying to make the seal I bet that is a good guess.)
I also discussed the port size with Andy Ricketts and the impact it has. This discussion lead to the manifold being blamed as the culprit for any problems...makes sense right
I agreed to run the car this coming up season with the cleaned injectors and make sure there were no leaks. At the end of the season the cylinder heads will be inspected again. According to Andy, Livernois stands behind their product!
OP, I hope you get this resolved in an amicable manner. You are probably much better off just moving on and having another shop repair them. My stomach turns over everytime I think about my car and dealing with Livernois at this point. I just wonder how many "bad batch" cylinder heads are out there waiting for other unsuspecting owners to discover.