Todd,
It took me a minute to figure out what you meant here but I pulled the back panel off one of my old basses and now I know.
The bass' preamp outputs are orange and violet wires. These used to be connected directly to the 1/4 jack (connection points 4 &

and then short jumpers continued from there to XLR pins 2 & 3. This makes the mono 1/4 mod a slightly more complicated operation. You have a couple choices...
Quick and dirty would be:
1- Unsolder all 4 orange and violet wires from the 1/4 jack
2- Solder two 20k resistors to connection point 4 of the 1/4 jack (you should use some insulation on the resistor's leads - can be made by stripping some other wire and sliding the results onto the resistor's leads before connecting)
3- Connect the other end of one resistor to both loose orange wires, solder and insulate thoroughly. (Hey, I said it was dirty!)
4- Connect the other resistor to both violet wires and insulate that.
What you have done is tapped off the signal from both the orange and violet wires on their way to the XLR jack, summed the two signals and made a mono output. Doing it as above would not disturb the XLR but would leave you with a couple floating junction points that would make Mica scowl...
The more proper way would be to have the orange and violet wires go directly to pins 2 & 3 of the XLR and also have the resistors terminate at pins 2 & 3. The resistors then act as the new jumpers to get back to the 1/4 jack (summing the signals when they meet at connection point 4). If you want to do it this way I suggest you start with a brand new XLR jack and try to emulate the factory's use of shrink wrap.
As for your phasing question ... if you are used to hearing the bass in stereo there will be some slight cancellation when you make it mono but there should be no shifting as such. Be sure that the two preamp output signals are at no point connected directly to each other - without the summing resistors. This could cause some unusual audio gremlins as the two outputs would be effecting each other in strange ways. If you have done the mod correctly the outputs from your power supply should still be discreet stereo but the the sound of both pickups should appear when you use the 1/4 jack.
Hope this makes some sense - I almost know enough to be an Alembic repair guy...
Jimmy J
(Toby, that's funny!)