Well, I would start at the basics, so yes, a warped head. Hears a quick check. Put your hand over the muffler. If the mufflers not like a 3.5 inch tail pipe, haha.
Does it suck your hand in?
If a head gets warped, it will try and share the cylinders, so the intake stroke of cyl 3, will suck in the exhaust of cyl 2, or vise versa, intake/exhaust strokes, ect.
Do you know the guys who shaved your head? are they good at what they do?
Also, was the head gasket made for shaved heads?
While the heads out to be milled, check valves. maybe the spring that holds the rocker arm is stuck, causing both 2 and 3 to hold a valve open a little, and if so, that would cause a compression leak.
Again, while the heads out, make sure the threads for the spark plugs arent stripped. you never know.
=D hope I helped