I will try to make this brief, but this issue does have a back story.
The bottom has a summary.

The car was purchased in NH by my wife (not at the time) and her father 3 years ago. Everything worked perfectly on the vehicle at the time with no prior issues.

Her father installed an aftermarket radio. He cut the entire harness without taking note of what each wire did or where it went. The colors of the wires are of no help as there are multiple wires of the same gauge and same colors in the harness. He eventually got the radio wired up and semi-working. 2 speakers did not work, the other 2 were switched left and right channels. Basically a mess.

Since then the radio DID NOT come on when the key was in the ON position. It also rarely worked when the emergency brake was up (changing the position of the brake would actually cut power to the unit in most cases). This also meant that while the radio did not have power, the electric top did not work. Only the rare times when the radio had power AND the emergency brake was up would the electric top work.

Fast forward to now, 3 years later.

Out of the blue, the stereo stopped turning on completely. No issue with the fuse. I disconnect the battery and pull out the head unit. Wiring is a mess. Loose and bare wires everywhere. I start the process of repairing it. I make a note of the current connections of each wire and cut them all. Used an AA battery to find the speakers. The constant and ground were both smaller gauge wires than all the rest (physically larger), but I connected the battery and used a multimeter to double check. The switched 12v I found because it became hot when the key was in the ON position. Found the dimmer/illumination wire. Disconnected battery and got everything wired correctly, connected and electric taped it all up. Looks beautiful. Connect battery. During the process the 15A fuse blew for the radio (unsure when this happened), replaced it with a spare and everything worked except the electric top.

Queue more issues. The digital clock and mileage now never turn off. The switched 12v, which worked appropriately earlier, is now "always on", keys in or not. Everything in the car stays on whether door is locked, key is in, or any other combination of events. I disconnected the radio entirely, but the battery still drains within a few hours.

I need some direction of where to look from here. I can also provide any additional information you will need.
A summary of the problem that I will keep updated is below.

Information:
1998 Cabrio w/ electric convertible top
Switched 12v is "always on" after dead battery disconnect/jump
Electric top will not function at all (all other electrical systems appear to work fine)
The vehicle had prior electrical issues centering around the radio
Clock and mileage do not turn off when driver door is opened as it did previously

Steps taken to resolve so far:
Checked all fuses
Disconnected the battery for 30+ minutes