Clutch and brake peddles not lined up

Might be clutch adjustment. These old girls only have one, the threaded rod at the bell/ fork. As old as these girls are, if you can't be certain the linkage is all original, I would not "not" expect this. In the early 70's, I swapped a diaphragm into my 70RR with a 340 swapped in. It had power disk brakes. There is no friggin way the two pedals were level, and especially with the difference in clutch types.