Andy,
Looks like theres plenty of room and meat on the crankcase to plug the existing holes and redrill to a square pattern , is there room on the cylinder base to slot the holes to suit ?
To plug the holes use an aluminium stud and screw it in tight with loctite or an epoxy adhesive then cut and grind flush, after the adhesive has cured mark out and redrill and tap the new holes - it wont matter if the new hole is 1/2 way over the old , they should hold ok just dont have loose fitting threads, and maybe loctite studs into the crankcase for the cyl hold down.
Stewart