I think the multi plug connectors use 1/4" spade terminals, correct?
Even if they don't, these connectors are all made so that the metal terminal is crimped on the wire and then the terminal is inserted into the shell where it locks into place. With either the right tool or an improvised one, you can remove the terminals (and wires) and re-insert them, there's a little metal tang on the terminal that locks against a catch in the plastic shell.
What this means, of course, is that you can go to a bike wrecker with wire cutters and clip the connectors off, remove the terminals, and insert your harness's terminals. You should be able to find good plastic bits, they don't degrade too much unless exposed to sunlight or chemicals - even really polluted air attacks them. I've done this here in Toronto, the wrecker had several badly hacked up hanesses and scrap motors that he didn't mind me harvesting from (for a price of course!).
Finding new replacements will be hard. There are thousands of possible different shells and they are really not available to a retail buyer, the market is OEM customers ordering massive quantities.
If you don't mind not being "original" there are plenty of standard multipin connectors you could use. The AMP CPC line has a wide assortment with 2 to about 30 wires and various sized terminals for different wire sizes and load currents.
