The output of your pickups compared to the output of the SA pickups don't matter a single bit at all, once they're 'in the system', it doesn't matter.
I actually use EMG pots and hardware in a lot of my custom guitars.
I use their specialty pots (EXG, SPC, RMC, Afterburner) with normal pickups all the time, and I also have a guitar with EMG pots and EMG pickups too (a Lukather setup).
When using standard pickups
, you use standard volume and tone pots
(250K or 500K).
When using EMG pickups
, you use their 25K pots
The 'secret' to using EMG pots with passive pickups is to always use the Afterburner or the PA-2 (they are the same pre-amp in different formats), once you stick that in, you can freely use any of the other pots they offer.
So your setup listed above would work just fine if you could stick in the PA-2 pre-amp as well (which is basically just a pre-amp on a mini-toggle switch).
A note though: I think you're OK with the Laces, but this is a lot of power to throw a regular SC pickup at, if they're microphonic at ALL...fuggedaboudit, you'll have the howl of the banshees.
If you're going to use the EMG gear, I would suggest shielding the guitar thoroughly, and use pickups that are inherently very quiet, which I think the Laces are indeed.
Here are a few of my custom setups, the basic layout is this-a-way:
Top Row Front to Back:
Bottom Row Front to Back:
EMG EXG/EMG SPC
Lollar Mini-Hum neck, Fralin 5% underwound bridge
Barden Strat neck, Don Mare 2324 'Nancy' bridge
Duncan Phat Cat neck, Harmonic Design S-90 bridge