I'm partial to Frankensteins myself. And I'm not aware of flex issues but sometimes ignorance is bliss.
Certainly not cheap if you want better than shade tree quality. But on V8miata.net I saw a gorgeous example of a NA with a 5.0 just go for around $11k (I think). There are deals to be had. But buying a newer more sorted car is not bad advice. ...if its a car you like. I'm not a NC kinda guy personally. But if a very nice MSM comes available I'm going to tick more than a few people off with my choice to drop my FM V8 parts into it and the FI drive train into my NA. You spend the cash...you get to what you want. Follow what you feel.