Is it just me or couldnt you finr a nice 90 degree peice of pipe and make one cut and weld it right to the flange?
I have the hobart 140 like Jet and I havent mastered it yet but I built my catback this past spring- first welding project I completed. Welds arent the greatest but they dont look like yours hehe.
I think gas welding really cleans up the welds, flux core is going to look like that but it could look better.
Read all of this and it will help you out on the settings and what happens with too much or too little heat, speed, etc.
http://www.esabna.com/EUWeb/MIG_handbook/592mig1_1.htm