The pulsating is most likely a tune issue. Many with speedies and Americans EFI versions have it as soon as the exhaust and emissions are altered.
Aside from your other thread about the speed limiter, are you able to load a new tune in your bike?

I have worked half a dozen bikes with this problem. The owners are always amazed at the difference, like a new bike.

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