OEM-style Connectors
From GummyCarbs
K&L
The K&L Catalog has a page for "Terminal Kits". These use connectors exactly like those found on Japanese motorcycles, including the pliable, clear vinyl covers. They're vastly superior to the cheap, hard-plastic-coated connectors you find at auto-parts stores.
I found the entire content of the K&L catalog scanned and posted online here. The terminal kits and connectors are listed in the Shop Equipment section, on the 8th screen.
I've had kit 34-8958 (the one pictured in the upper, left). It's worked well for many years now, though with recent work I'm out of some connectors. The supplied crimping tool works well when used correctly.
Vintage Connections
Vintage Connections sells OEM-style terminal kits.