Fuel issue? Vacuum issue?

Okay, need some help. I'm at my wits end. My dad had given me his old 2002 vtx1800. It has sat for two years so it didn't run. I took off gas tank and emptied it out, replaced fuel pump inside tank, changed fluids. Started it up to run for few minutes then killed it to add the last quart. Then it wouldn't start and then i flooded (fuel coming out exhaust) . So I did some googling, and come up with replacing the fuel pressure regulator. So I replaced it, changed the FPR and changed the fluids again. Start up just fine. Killed it to add last quart, now the dang thing won't start again. I didnt touch the throttle when starting either this time around. If I let it sit a minute, with the key off and run switch off, then on again then start it will run a second then die.. suggestions please! It's just odd because it idled great after replacing the fluids the first time, and then again after replacing the FPR and fluid change, but when I shut it off I haven't been able to start.