I apologize I did not see this in your first post. All cylinder 85-89 are the same dimensionally. The pin height changed from 86 to 87. So it comes down to which piston you are using not the difference in a long or short rod. My builder Pete at Hybrid said he commonly runs the piston out the top and cuts the head to correct the squish.
Having the cylinder as low as you can mount it on the cases & then running the piston out of the deck is the simple way to do it, not the proper way as some will say, but theres been so many strokers built that way I lost count.
One thing that will be a problem, if any port work at all has been done to the cylinder your intending to use.
All porting work will raise the roofs of the ports when completed & if you add a stroker crank into the mix with an already ported cylinder, it will turn the cylinder & engine build into a drag type engine, because of the high port degree openings, so you want a cylinder that the ports have not been touched & then do the cylinder porting after the stroker is added.
Another thing you need to check for, if you go with the cylinder mounted to the cases with one base gasket, so it will be as low as you can get the port windows.
That +4 stroker will add 2 more mm of travel of the piston at TDC, so you'll need to check the piston skirt on the exhaust side while at TDC to make sure the piston skirt not uncovering the floor of the exhaust port.
I dont know if any of you seen the thread on .net where Rob was building one of the 200 engines, but in that thread it was showing pics where the exhaust port floor had been welded on to raise the floor at the edge of the bore, then machined to the proper floor height, so that the piston skirt wouldnt uncover the exhaust port floor while the piston was at TDC. Just saying so you get an idea of what 'm saying.
My deal is, I've never had something new to work on, has been 90% of the time been something somebody else has done & then I had to correct it so it would perform to the customers level, so I've seen a lot of different types of engine combos & had to walk backwards through how it was engineered. I guess you could say I've been through a school of hard knocks figuring out a lot of builders engines.
A Sparks engine is the most mind blowing of all & if you try to change it in any direction, high or low, you'll end up carving into a coolant jacket.
Ol Curtis is smart now, but you take a man that going through life has had to take nothing & make something out of it, he'll dig until he figures it out.
Once you've got the cylinder placement figured out, I would say find a cool head & get a custom dome machined for it or either a CR250R head & have the dome on it machined so the piston can run up into the heads squish area.
The CR head is thicker die cast, will have the OEM TRX look, so the dome area can be machined on it more than a standard cool head type dome.
Cool head dome has cooling fins machined on its outsides, so if you go to carving on the squish area to much you'll end up killing it, reason I say get a custom dome machined.
What would be nice, one of the ESR heads with the stud pattern to match the OEM jug & then a blank dome to machine on to get the proper squish.
Neil