I'll try to help.
That crank deal on e bay is kinda confusing, cause if your going to use it, what piston could you use that wouldnt hit the crank tins. Maybe I've not built enough different types of 250R engines to know, so the only piston I could think of would be the old 85/86 version.
As Tony stated, all years of the TRX250R cases will interchange & can be mix/matched with different year model internal parts.
Some differences in how the cases are cast should be noted, like the width of the front engine mount is wide cast & other years it is narrower. The narrow type front mount, say like if attention is not paid to the engine to frame mounting bolts & most have for some reason came loose, that little narrow front mount could break off, but theres been very few that I have seen broken.
The 85/86 cases, how they are cast, they are thicker cast directly under the crankshaft area, so they are good to use like if your building a stroker crank build that the cases must be trenched, from using an abnormal type of con rod that the big end of the rod not clearanced. By those being thicker in that area, if trenching is needed they tend to retain a bit more strength because of that thickness.
The transmissions, early 85/86, some of those gears are different ratios than the 87 & up gears. The ratios between the years I do not know, just that some are different. Early year gears were more prone to busting, reason why could be many reasons. Maybe they were hardened to much, so they were in turn more brittle or maybe to soft, not hardened enough.
I do know this about them, the ratios of the early years, those ratios when used with a high compression big bore grunt engine build, in a race when you shift to third, every body else on the line is history, but you have in the back of your mind wondering when they will bust.
The 87 & up being the best, will last the longest & has the closest ratios, but one of those can still be busted.
If there has ever been a late model transmission been through a test, it has been my daughters, because once she leaves the start line in a race, that clutch lever not touched up shift or down shift. I guess she must think its an automatic, but I know she knows better. Since 04 her engines only been rebuilt once & we've only had one gear to bust in all those years & believe me, in those years the engine has been beat on racing national level & local EDT racing.
Do not, mix & match transmission gears from different years.
If you have a problem with a trans & need to replace an item, do the research & be sure to get the proper year replacement part. Keep 85/86 parts together & dont mix with the newer years.
You can to some extent research, go to like an OEM parts site, pull up the micro fisch & look up the transmissions of different years & it will list the gears & how many teeth that each has. Make a list of each year & each gear & the teeth count & you'll know which gear matches up with which year model.
After you have that list in hand, if you pull a transmission out, all you'll need to do is count the gear numbers to know which year trans your dealing with.
TRX250R OEM cylinders, if you measure them they all measure the same from base to deck, can be mismatched between years on all year cases & just a mater of using the correct year piston & crank combination.
Neil