Standards for vehicular lighting connections
The AC output voltage of your generator(s) varies under a constant resistive load (see http://www.seeedstudio.com/wiki/Bicycle_Dynamo_With_Bracket_-_6V_3W#Specification). What are you planning to power with your "electrical system"? Traditionally one would be powering incandescent lamps, which don't care whether they receive AC or DC or at what voltage (when you slow down, the lamps dim). The more sophisticated the load, the more voltage regulation you will need. Rectifying AC into DC requires a simple diode bridge. Then, you would obtain regulated DC by using a voltage regulator (for example LM7806 if you want 6VDC). Surround the 7806 with appropriate capacitors, see the data sheet. Note that you can't get regulated 6VDC from rectified 6VAC -- the 7806 requires at least 8 VDC of input to get 6 VDC output. You might also want to use a largish capacitor or two to keep the DC voltage constant for brief intervals while you are slowed or stopped in traffic. If you are trying to power a device such as an Arduino or cell phone, you are probably better off charging a battery and running the device from the battery.

As far as connectors, I would use Molex connectors, one wire at a time (toss the nylon shell), use heat shrink tubing (as you are already doing) on the individual wires and also on pairs/bundles of wires. Hopefully you won't be disassembling your wire harness all that often, and this arrangement should provide adequate protection against strain, moisture, and vibration. (In moist environments put a dab of silicone sealer under the heat shrink tubing with a toothpick.) For servicing, just slice open the heat-shrink tubing and unplug the Molex connectors.