Since this isn't a First gen Roto engine, then any special engine will be fine. There are 2 lengths for Model 3 4 and 5. Stick with the short shaft and thread since its roto and doesn't need to pass through a base exhaust. You can still use that shaft if its straight. Check the new bearings and see if they are tight, if not re punch or use retaining compound on the shaft only and replace the bottom crank half. Its getting harder to get good cranks, especially for Rotomo. At least half mine have been previously punched, but I cant afford to throw any out, just because of this.

Make sure you do your small end bush, as they are always worn.

If the crank rocks excessively at TDC then change it.