My strato work was limited to that 450 with all the inherent problems of a 'big bore' on a small chassis. However, I did learn a heap by overcoming all the problems.
I did cut my piston to take the blowdown out to 16 degrees, coupled with the notches on the piston to increase the area, the saw flat screamed. Unfortunately, I have a 13,000 limiter on the coil. Hell, with the 14 degree blowdown and the other work, I can hit the limiter quite easily. So, I went conservative for a work saw and stayed with 14 degrees (plus the notches which seem to work like an extra 2 degrees).
If there is no limiter problem on the 562, you should be feeling some serious revs.
As I mentioned before, I'm in the matched strato/intake timing camp. The crankcase compression can't start until both strato and intake ports are closed. Having one with a shorter duration simply restricts the ability of the engine to flow the 'intake' charge.
As it was on the 450 the intake was 144 and the strato was 154. Further, the strato conduit was 13.5mm and the carburetor intake venturi was 11mm. Now wrap your head around what was going into the cylinder - LOTS OF AIR. Yet, the fuel mixture was just fine at the time of combustion. In other words, when it got down to the moment of ignition, the turbulence of the air and fuel mixture had formed a homogenised air/fuel mixture in the combustion chamber. - When you go back in, if you need any more intake duration, I would go with increasing the strato timing to match the intake. You will still have the same base compression, but will have picked up more flow.
I'd check the strato intake as it comes into the cylinder. I had a flow restriction from the piston at TDC. It didn't take much on my saw to increase the strato flow about 30% just by trimming the piston edges that were in the way.
I'm anal when it comes to flow patterns on pistons. They tell me a lot about what is going on in the cylinder. When you go back in, check that area of the pop-up that sits in front of the transfer flow. I noticed that the 450 had a really nice flow pattern from the way the transfers entered the cylinder. It may be that flow pattern over the pop-up will indicate that you could trim some of the pop-up near the transfers to clean up the flow pattern. You may not need to completely cut down the pop-up at that point, perhaps just smooth out the edges so that you get a clean flow.
The last thread on modding the 562 showed some problems with getting the stock carb to flow enough fuel. I had the same problem on the stock 450 (after boring). It appears the factory is still playing around with keeping the mixture on the lean side. You should check the metering lever height because it in all probability will be set low and you may have to drop the POP to get some more fuel flow.
Nice work by the way, that is one purty engine.
EDIT: When you get a chance, check the size of the venturi on the carb. The 445/450 had a 11mm, the 570/576 has a 13.5mm. I expect that the 562 has something like a 12 or 12.5mm venturi. The C1M carb is on all these models, so the larger 576 carb would fit. Someone may want to swap the carb or bore out the 562 carb.