As long as you are below 68MM bore, you can use the 85 cylinder & Long Rod crankshaft with no spacer plate needed. If going with the 85-86 piston kit and Long Rod; use a 3/16" spacer late + two OEM base gaskets (spacer not needed with short rod crankshaft). Keep in mind neither setup is better than the other (other cylinder options like 87-88 will improve performance), except the 85-86 piston kits allow you to go to 69.50MM bore.
For WOODS; the emphasis should be on Low to Mid range power, therefore the Long Rod crankshaft is a better option than the Short Rod. Going to a stroker crankshaft like +4MM is your best choice as it increases low to mid range TrQ & Power....an OEM BDT276CC aka 68MM (67-69.50) bore x 76MM stroke (+4MM) is a great WOODS engine with a lot of TrQ & HP down low for WOODS...winner of many MX, XC & TT National events the last +7 years.
As American Opel-Martin stated; the 85 cylinder is fine, however; each progressive year Honda made small subtle changes to each cylinder. The 86 is slightly stronger than the 85, the 87 is a good improvement in reliability (less piston wear-longer life), the intake design & support as well as exhaust track angle & volume, the 88 cylinder (88 is 89 cylinder) is the best of all since it has all the subtle changes Honda incorporated over the years of development.
On builders; perform your due diligence, start with this forum, FB, and look at whose building winning race engines across MX, TT, XC, WOODS the past 7 years. Also who is available to answer questions, who stocks all the 250R parts, and who promotes 250R's, travels to National events, ect...the answer then becomes obvious.
Any questions PM or call me directly at BDT Motorsports, here to help as needed.
Great to read your Dad & you are involved as a Team; "he ports & you polish"....awesome. Best of luck,
Carlos