In a live league where there may be more running, I am not sure if I want to use the 09 Mauer with the D+ arm at catcher. I was thinking the 06 with the 347 avg and A+ arm. Salary is not a factor, I won't reach cap anyway. Is the extra avg and homers worth not being able to stop a running game in live?

Definitely go with the A+ arm...even with the "Hold Runner" setting in Live, stealing bases is much more frequent than in a sim game.  Everyone who has a decent SB% is essentially going to run every time on base.

I have the '06 Mauer now in a 120M league (home park is Miller Park [-2,0,0,+1,+1] PF 0.98).  Keep in mind that he doesn't have a lot of RL PA.  I bat him 8th or 9th and he does ok.

His current stats:
66 games
267 PA (fatigue is still at 100%, he's currently on pace for 7% more PA)
232 AB
.250 BA
.345 OBP
.358 SLG
15 2B
2 3B
2 HR
41 RBI
34 BB/ 29 K
He's thrown out 15 of 54 base stealers.

And for what it's worth, he's grounded into 12 double plays.

I have used '08 Mauer in a 100M league and he went .293/.376/.384 and threw out 32 of 129 base stealers.