Generally speaking what I've seen is that it's ok to apply in advance, but I can't be sure for your particular situation (I didn't even know that VN did 3 month visas.... are you American?).
I recommend posting this on the aseannow or tripadvisor forums -- probably the latter, as they're quite good with visa questions. Or at least r/VietNam
honda supercubs might be a nice middle ground. 70cc with gears but no clutch. it's basically a semi-automatic.