So I have 3 lvl 60 jobs and a few lower level around 40 that I would like to eventually level. I am in heavensward around 51 lvl quests. Is using my lvl 60s fine or would it be more efficient to level the other jobs first and continue MSQ with those jobs until I reach lvl60 MSQ quests?

The only real point of concern should be that you don't hit the level 90 cap and start literally losing exp from the story quests. Beyond that, the 'optimal' number of jobs to level just depends on how you're playing.

If you're plowing through the MSQ as a primary source of exp, you're probably fine just rotating 2 or 3 jobs during that process. If you're completing every sidequest along the way along with other exp-heavy activities (daily hunts, beast-tribe quests, roulettes, etc), then you'll probably want more jobs in the mix.

Keep in mind that you receive bonus combat exp (100% before level 80, 50% after) when leveling jobs that are lower than your current combat-job cap so it'll be easier to catch up with the other jobs you want to level later on.