The schematic is based on the assumption of a negative ground. I've seen a positive ground three wheeler, forget what make. The voltage regulator is a heavy duty automotive grade. Hopefully there is a battery? All bets are off if this is solely a magneto driven circuit, haven't messed with them. Not sure what extra requirements are necessary.
Yes the numbering is correct, 1st gear goes to pin 1, 2nd gear to pin 2 etc.
The program port is for in circuit programming (ICSP) of a PIC microcontroller. This is a common way to do it, and relieves shuttling a chip back and forth from the circuit during prototyping.
Like I said, this not a shortcut. You need to program, or find someone to program the code. Then, the code needs to be burned to the chip with a programmer like a PICkit 2 or 3. If that is not in the books, then maybe someone will come up with an analog solution for you.
10k pullup resistors for the gear selector inputs should be fine.
The SSD resistors were deliberately left out, and depends on type, and color of led display purchased. The data sheet will give drive current, forward voltage, and brightness of the leds. It may pay to get a couple different ones to compare, like Avago, Lumex, etc. Avago advertised a daylight viewable
AlGaAs SSD.
Don't be confused about the SSD pin numbers, as the schematic uses a "generic SSD", and will disagree from the datasheet. If you set the pcb as remote from the SSD, I wouldn't trust the handle bars as ground. Chassis ground should be O.K.?