68 Evinrude wiring harness help!

[68 space twainer]

I recently inherited a 1968 Mark Twian w/ Evinrude 100 S w/ electric shift. I'm in the process of replacing the wiring harness and have ran into a bit of an issue. According to the few sites I've sites I've checked with, this outboard uses the 413-9909 wiring harness. I ordered one and began installing, however, towards the end of the harness (near the pulse pack) I have a dilemma. The old harness has (1) 3 pin connector, (2) 2 pin connectors,and (1) one pin. There is also and existing harness that goes from the vacuum switch (2 pin) to 2 singles near the pulse pack. The new one has (1) 3 pin, (1) 2 pin, and (1) one pin. So I am a 2 pin connectoe short at the voltage regulator, and not 100% sure as to the 2 single connectors coming off the vacuum switch.
I was curious if anyone has replaced this harness and had similar issues. I have a service manual and wiring diagram, althought the new colors don't seem to match up. I'm also hesitant to start "modifying" my new harness........Any help would be greatly appreciated!!!!

Thanks!