Chris I would go with the MTB. You said it's very comfortable, and that's good!
It will make you feel safer. You said it's cheesy, but heck that could make it less
likely to be stolen. I prefer comfort over anything else, (well not safety) while
commuting. You state the "fuji is a work in progress" well bike communting for you,
right now is a work in progress. I wouldn't try to tackle to many things at once.
I might suggest biking 3 days a week for starters, leaving the other two days to
bring all your gear, clothes, etc, to the office, and to figure out, what work, what didn't. soon enough you'll be addicted enough to try the road bike.
truthfully, there are days I ride my plain jane hybrid because she's just fun!
take care, happy trails!