So I pulled my cylinder off to see how things are going inside. It has a good few hrs on it and has actually run pretty well. I noticed exhaust gas showing signs all over the lower end and transfers on the underside. Started to talk to a few people and did some rough measuring. What I have come up with is I believe the piston cutaway on the bottom of the piston is rising above the aux. Exhaust port at t d.c. and allowing exhaust gas to re enter the crankcase. Thoughts and opinions? Im going to contact eddie tomorrow if possible and see what he says but I see this as an issue. I did a rough illustration of what I believe is happening. I cant get it to load right side up the boot shape is the piston pin area and the line tagged problem is the piston cutaway. 
You are correct in what you are thinking. I tried for quite a few years to get LA Sleeve & CT to change the piston design, so to stop the port linking, but it fell on deaf ears.
When I spoke to Eddie about the port linking issues, say a year after he came out with his own cylinder castings, he changed pistons & got his on design you see being used today.
The issue when your using the old design Pro-x piston, from the piston being machined to much on the sides to lighten them, lighter piston, more hp output. If it was just a slight opening or just opening up into the wrist pin hole, then the effect wouldnt be as bad, but the length of the machining on the pistons sides & the aux exhaust port window, the duration of the open area is to great during the cycle of the piston at that time in the stroke.
Do know though, the linking issues not as bad as it was a few years ago, because of the design of piston Eddie is offering today.
I'm thinking it was back in 98~99, maybe 2000, did a test on a 310 Pro-x cylinder. Welded up the aux exhaust port of the sleeve & then going back & opening up a smaller window so that there would be no way for the port to link.
That little 310 at a national TT event, was sitting in third place behind Tim Farr & Shane Hitt until the small o ring on the head dome melted & blew out the coolant.
It was part my fault, because I took time & watched the rider running the R which had a 450R as well & was spending all his attention to the 450. If the 250R had been attended to like normal, the radiator would have been checked & would have been found the coolant to be low. By it not, when it went out for the main & the coolant low in just a few laps it over heated & melted the o ring ending that little 310s life.
He ran it till it wouldnt run no more, it pure turned the crank black it go so hot, but it was gittin it done for a little while.
That test, proved to me how big of an issue that port linking ordeal was on these cylinders & something needed to be changed, but deaf ears wouldnt do anything about it until I went over it with Eddie. In less that 6 months time after our talk, ESR started offering the piston design you get today when you order a cylinder kit, so we got to give Eddie credit for doing that.
What would really be nice, if the machining on the piston sides were just like a CR250R piston, then there would be no linking at all.
Today, when I'm working on the aux exhaust port windows, I do not touch the rear part of the window, not widen it any at all so to prevent as much as I can any port linking. Its all I can do other than welding up the window in the sleeve & then re-cutting the window.
When you order a new replacement sleeve for these cylinders, should you have one sleeved, the new sleeve even after the CNC machining is complete, the window opening is cut to far around because of the angle of the cutter.
Heres something odd to think about, say your building a 270cc OEM TRX cylinder using the YZ250 piston, specially on a cylinder that is all ready ported. If you check that build when the piston is at TDC, you'll notice the skirt of the piston is uncovering the floor of the exhaust port maybe like a mm or two, but it has no affect on output & if anything its helping.
I dont know how it could be tested other than on a dyno & two different cylinders to check. My guess is, that at that part of the stroke the returning wave in the pipe is pushing some of the fresh intake charge spent out into the pipe back into the crankcase & acting like a turbo effect. I have nothing to prove this though, but I do know every one I've built that ended up with that little piston skirt gap will tote the wheels out of a corner & make for one happy rider using it.
Neil