Easiest will be to treat it like a Sportster and fix what's different. T&O 4-5/8", replica XL rod set (1954-81). Any year K/Sportster pump will fit but the years closest to you may be less plumbing problems. Increase the breather timing to late XL specs or use the 1972-76 pump. With some work skirt oil can be plumbed into the original flange holes through the plugs. Replica K pistons. Any matched pair of tall cylinders - be very careful about bore size, many of these were bored to 2.875" for Scout/Atlas pistons and need sleeves so listen closely when someone says "the bore is std." - that may mean the Scout pistons are marked std. You need an actual measurement. Many are also cut for 45 exhaust valves, not easily fixable.
Transmission: the whole point is to use the 1956-69 dry clutch trap door set-up, which has been done (I had one but didn't do it). Easiest is just used parts from someone's basket case to borrow as a dummy for fit. Ratios can be selected after you know what you need, but here are some choices: