503 missing revs

I wonder if anyone can help me? My free air 503 DCDI is down on revs following a complete strip for crankshaft replacement. Before the work I was getting 5900 rpm static now it's 5500 at best. The running pattern is:

The fuel system has been substantially renewed with new tubing, filters and a serviced Mikuni pressure pump. (There is also a Pierburg electric pump.) A fuel pressure test shows at least 0.2 bar being delivered at all times, with the Pierburg adding approx 0.3 when it's turned on. 

The timing has been checked and re-set. The ignition system is within Ohm limits and new spark plugs fitted. The carbs have been overhauled with new jets and needles and statically balanced. I've double checked that the part numbers are correct. The B gearbox has been serviced and contains the correct type and quantity of oil. The prop has been tracked and the pitch has not been changed. A leak-down test of the crankcase shows that it holds -5 inHg for at least 30 mins. A compression test up top gives 123 and 129 psi.

The cylinders have been bored out to first oversize with piston sets to match. Cylinder wall clearance seems to have been a little tight on the first start up (all the honing disappeared and was replaced by scratches) and so I had the cylinders taken out further, but still within the wear limit. The crankshaft is genuine Rotax and I checked alignment before fitting it. I've been using E5 unleaded RON95 petrol with my usual 2 stroke oil. The Rotax break-in procedure has been followed and the engine's run about 2 hours now (all on the ground).

CHT and EGT are well within limits and fairly equal.

Interested to know your thoughts.