The 1664 was an option for the Meade refractor mounts as was the 1697. Here's a quote from a PDF I found online for the refractors:
"Motor Drive Systems: Factory pre-installed on all Meade apochromatic models as standard-equipment are two DC servo motors, one each inside the polar and declination axes. Installing either of the optional drive systems requires no more than a few minutes and entails simple plug-in connection of the declination motor to the power panel and attachment of the power panel to the declination casting. Alternately, either the #1664 EDS or #1697 CDS may be factory-installed at no additional cost, if requested at the time of order. Once installed, the drive system is totally integrated to the mount, with no motors or electronics externally visible. Either drive system, #1664 or #1697, may be added to any Meade APO model; each includes a 25 ft. cord and adapter for operation from any 115v AC outlet."
You can certainly use 12V for either the original 12V drives or the newer 18V drives, the motors are the same. Meade bumped the voltage up to 18V for faster slewing and didn't make any changes to the electronics. That was part of the reason that the caps had a tendency to blow, because they were being operated with less of a safety margin. It might not have been a problem if Meade hadn't used an unregulated 18V power supply that could often spank the caps with voltage spikes very close to, or over their maximum operating voltage.
Conventional wisdom with those old systems is to change out the caps regardless, because there is no way of knowing how many voltage spikes the capacitors have taken over their lifetime. Your situation is a bit of an anomaly because you say your electronics are "new" so it could be assumed they haven't been abused by the voltage spikes. It could be argued you'd be perfectly safe running your system @ 12V which is the design voltage. My only concern is I've read the epoxy used in the capacitors dries out over time which may lead to failure. The problem with these old style capacitors is they fail by shorting out which can cause damage to other components. Newer style caps can still fail, but they don't short and go up in flames.
Since you say you have two sets of #1664 electronics, you certainly have a back-up should one fail and that would tell you if you needed to replace the caps in the spare set. I'm not familiar with what kind of hand controller the #1164 uses. If I had to take a guess, I'd say it was different than the LX200 and #1697 controller so if you don't have a #1664 handbox, you may be stuck until you find one.
I recently put my LX200 scope into storage, but am still using my LXD650 with the #1697 CDS system. I should be visiting the storage unit in the next week or so and I'll see if I can easily get to my LX200 handbox. If I can, I'll grab it, bring it home and try it out on my 650. I suspect they are the same because the controllers are just dumb input/readout devices and the software is "almost" the same for the two mounts, the difference being no Alt-Az option on the #1697 and differing start-up positions. In my mind that shouldn't effect how the mounts communicate with the hand controllers. They look identical but they do have different firmware numbers so I'm not 100% sure.