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If you've got a voltmeter, test across the battery with the engine running. That'll tell you quickly if the alternator is charging. I doubt the other lights need to be changed back unless something's acting up. The error free ones might work. They're supposed to look enough like a standard bulb (electrically speaking) to not trip dead bulb alerts on cars that check for that. Seems like they'd do the same here.

I picked up an OEM style aftermarket remote. Terrible quality, the portion that loops through a key ring has broken in multiple places. Any other style/model year remotes that will work? Im using the KOBUTA3T right now. Looks like this one https://www.ebay.com/itm/Fits-1999-2000-2001-2002-Mercury-Villager-Keyless-Entry-Remote-Key-KOBUTA3T-2x/112769706650

I had the same problem some of you were having getting my keyless entry into programming mode. No matter what I did I couldn't get the lights to flash. Skip forward a couple years to today, I was checking fluid levels under the hood before a road trip and saw the control box on the drivers side that said Keyless Entry on it, and thought maybe I should take a quick look under the panel. Everything looked OK - the brown box was where it should be. I tried to remove it but only got it part way and didn't want to force it and risk damage so I just stuck it back into place. It felt like it reseated so I hopped back in the drivers seat, locked the doors, stuck the key in and out, in and out, and right when I was about to give up for the last time it flashed. I turned to aux, hit a button on the keychain and I NOW HAVE WORKING KEYLESS ENTRY!!! I'm pretty excited.