While it is hard to tell from pictures, I can't see too much wrong with the scavenge patterns.
Assuming heaps here, I take it (from what you write in regards to lower port timings) that some material has been removed from the cases to lower the port timing.
This is something I do reasonably often (on certain cylinders), and, as you have found, the piston then obscures the exhaust port by a few mm's at BDC.
I do it to get certain cylinder blowdown times closer to suitable, and as such, have to raise the exhaust port to compensate (a design flaw)
First I was quite worried about this, but it turned out the gains from the correct blow down times MOre than ofset any losses I precieved I would get.
I am guessing who ever designed your engine (wobbly?) has designed it as a whole unit, and a process was followed.
Looking at your scavenge pattern/pipe design, it would be my opinion (I think you mentioned previously as well) that you are running a larger crankcase volume ( with a ratio some where around 1.3 or so)
Such enviroments (lower primary compression) seem to assists even older designed scavenge patterns in being more "efficient", also combined with the now lower port timings.
As a rough example (and VERY VERY VERY big generalisation) using such set up methods I would expect to have exhaust duration around 191 Deg and transfer duration around 130 or MAYBE 131 Deg.
Is that somewhere near what you have?
Also what are your blow down times?
Maybe as you suggest it would be worth revisiting your port timing, and as a test, space up the cylinder to get the port unobscured and degree that as well.......... just as a comparison......... correct blow down times are dependent on operating RPM's (exhaust port duration) if the duration has been lowered, but the blowdown time is the same, then there is a good chance it is now "mismatched" (not enough blow down time) which will have the effect of a great torquey engine (sound like what you have) that has a narrow peak power delivery, which falls off abruptly.
IF I am correct (I'm not saying I am) then you may well need to space the cylinder up to get the blow down times to match the exhaust port duration (at the cost of low end torque sadly)
OR...... you could raise the exhaust port height a few degrees........ and leave the transfers where they are....
In my opinion, the first thing I would do is measure the blow down time, and base the exhaust port duration you want on that time calculation.
I wouldn't be overly worried about the shrouding of the exhaust port (as strange as that sounds!)
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