This may not help you at all but just for the record, my 1999 Navigator did in fact have two amps, one for the regular speakers and one for the sub. The sub amp was attached to the same housing as the subwoofer. So we do know that Lincoln did in fact use two amps at one time at least.

PS. It was the Alpine premium system.

I do have a 2009 MKX with the THX that sounds great. Let me know if there is anything I can check for you.