Well...I dont want to get into referencing any company in particular...but a couple other things to look for are....work on the rod...IE knife edge on the leading and trailing edges of the rod. Also...some folks open up the oil port in the rod a little, to allow more oil to get to the bushing. Also...the crank might be modded. Some folks drill out the port in them larger (if you are dealing with a CVRM, I hope this is not the case...since it is not rare to break a crank in one of these engines...so I would not want to have anything done to one I owned that might make it weaker). Also, where the fuel/air mixture exits the crank, some folks will cut a curved exit on the rear of the crank.
I guess, in short, without a list of what a company said they would do to the engine...there are a lot of things they might have done just to call it a modified engine.
As to knowing a reputable company that does these kinds of mods...not me, I dont know one. But, I think most of them would charge more than the CVRM costs brand new to mod an engine...
I dont know if I am allowed to mention other websites on here...but international waters might be a good place to ask for a recommendation for an engine modder.
http://www.intlwaters.com/
Sean