I would suggest doing the regulator/rectifier mod. if you have not already. It seems like the procom is sensitive to low voltage, it works but not as well.
If you are going to make program changes (which is really easy on these)try retarding the timing at low rpm, that should make it easier to start.
and are you using the TPS?

05 speedmaster - 1100cc, 11:1 racing pistons, Carillo rods, thunderbike cams, ported and polished head, 2mm over intake and exhaust valves, Barnett kevlar clutch, scepter pipes, oversize manifolds, 45mm HSR's, TTP stage 4 firestarter