Is a prenuptial agreement valid when man/woman cohabited rather than married? Does it protect against quantum meruit when relationshp ends? Is the 3 year statute of limitations instituted?

Depends on how its worded. Since, by definition, a prenup is an agreement for distribution of assets IF a marriage ends, then there would, seemingly, have to be a marriage to end.

However, ANYONE can draw up an agreement to say anything (as long its it doesn't violate existing law). So if you want to draw up an agreement that says something like:

John and Mary, agree on this date to cohabitate. If and when this cohabitation arrangement ends, any assets that each brings into the cohabitation will revert back to the original owner. Any assets acquired during the cohabitation will be divided equally.