What size wood to use for garage loft

If the existing setup works, I don't see any reason why it wouldn't work with new doors instead. One down side to this setup though, is that doors without jambs aren't that secure and could probably be kicked in fairly easily. If it were my garage, and I didn't want a standard fold up door or a roll-up, I'd probably put in 2 larger barn style doors, or if you have the space, one of those sliding barn style doors that has an overhead track to slide on.

Assuming open flame heaters are allowed in a garage in your area, carefully check all clearance requirements for the stove and flue. I would encourage you to adapt to triple wall insulated flue pipe at the ceiling of the first floor and stay with insulated pipe the rest of the way. Do not attempt to change back to single wall pipe.

You may want to install a couple of floor registers to help take some of the warm air from the first floor to the second floor. Remember, heat rises, and depending on how long you run the stove, the heat will eventually fill the second floor. Some simple electric fans can also be placed strategically to move the warm air around and even out the temp in the building.