Perkins Fuel Injection Pump Timing Problem

[dancamp009]

I just installed a rebuilt perkins hydraulic fuel injection pump on my Perkins 4-108 inside my 40' sailboat. Before I installed the IP, I also installed a new electric lift pump and blocked off the old mechanical lift pump, because after removing it, it no longer seemed to work.
My original IP main shaft broke after 10 hours of rough water use with a dirty diesel tank. (I also cleaned the tank and all lines, and rebuilt all injectors).
I did not turn over the motor after removing the old IP and did not check that #1 cyl was at TDC when I installed the rebuilt IP. After installing the rebuilt IP and aligning the timing marks perfectly, the motor barely started and then ran VERY poorly (smoked, clanked) until I twisted the IP back 5/16" above the original timing mark. It now runs fine, with a few exceptions. 1) it now produces a little blue/white smoke out of the exhaust (unlike previously with the old IP), 2) it now only allows up to 2000 rpms under torque (5 knots max in the calm) and 2500 at idle (it used to give 2500 rpm's easily under torque and 3000 at idle).
I will try readjusting the timing again today, but I do have a couple questions maybe somebody can answer.

1) Could this IP have been rebuilt incorrectly (out of time by one notch)? Why else would I have to change the timing so drastically for it to run decently? Or could I have installed the IP one complete engine revolution out of time (on the exhaust tdc)? And if so, would the engine even run?
2) Could the governor have been set too low and is this is why it doesn't get more than 2000 RPM's under torque? I used to get 2500 or more if needed and get more than 5 knots in the calm.