Alex,
There is an advantage to using self-aligning rollers on the drive side of the engine, but not in the gearbox. It would be o.k. to leave them be if on the layshaft, but I would have reservations about using them on the mainshaft since that is made up of two pieces on your gearbox design. The standard radial bearing(s) may lend some rigidity to the mainshaft that the self-aligning bearings would lack.
The correct bearings should not be difficult to get. The layshaft are standard metric ball bearings. The mainshaft bearings are an obsolete imperial size, but are still made by RPH.
-Doug
