It is possible that prior problem with the trunk switch could have been a short and then the wire burned up more and caused a larger short, but that doesn't mean that it is. The best thing to do is test both for the drain on the battery.
Test for a drain on the battery by a using a 12-volt test light or voltmeter. Take a full reading across the battery posts to get total battery voltage. Write that down. Then disconnect the negative battery terminal and hook the 12-volt test or voltmeter with the positive test lead on the disconnected negative battery cable and negative test lead on negative battery post. Turn everything off, close the doors and if you have a hood light remove the bulb. With the negative battery terminal disconnected and a test light or voltmeter between the cable and post see if you have a drain showing on your test light or voltmeter. A light on the 12-volt test light or voltage reading on the voltmeter indicates that something is draining the battery. If so start by unhooking the small wires at the alternator and see if the test light goes out or dimmer or if the voltmeter drops in voltage, hopefully to zero. If the 12-volt test light goes out or the voltmeter now reads zero or less than 0.2 volts then you have found the short. If the voltage is not zero on voltmeter or test light does not go out, the short is somewhere else. If the voltmeter just drops some or the 12-volt test light just dims a little you still have a you have a drain there but still a drain somewhere else so start pulling the fuses 1 at a time and when you do find out when you pull a fuse and the drain gets lower then put the fuse back in hook up the battery and make sure everything on that circuit works. Let me know which fuse you pulled and I’ll upload the wiring diagram so you can check everything on that circuit and make sure that it works. If something doesn’t work on the circuit that is causing the drain then it may be short-circuited with another circuit of shorted to ground. That may help find where the short is if something don't work. So with your 12-volt test light or voltmeter test the wiring to whatever doesn’t work to find out where it has voltage and all of a sudden looses voltage and then repair that spot. If any drop some or allot write it down which fuse it was and if using a voltmeter write down how much volts it dropped. Remember if you have to keep the door open to pull the fuses just push in on the door switch after every time you pull a fuse and go to look at the meter. When all fuses are pulled and the alternator wires are off you should have no drain and written down everything that was causing a drain. If you still have a drain with every fuse pulled and the alternator wires off, then it must be something that is unfused such as anything that may be fed from the light switch.Last if you have all the fuses out and still have a drain disconnect the big wire at the alternator. If the drain now goes away you have a bad diode in alternator.
If the fuse keeps blowing, install an automatic circuit breaker in the fuse spot for now so you can test that circuit.
On the trunk switch, is it the Trunk Lid Opener or the Trunk Lid Pull Down?
What is the name of that relay?
Here are some wiring diagrams.
For the 1993 Lincoln Town Trunk Lid Release, click here.
In this diagram, I see a H 30A fuse in the engine comp fuse box.
For the 1993 Lincoln Town Trunk Lid Pull-down, click here.In this diagram, I see a #1 fuse 15A in the I/P fuse panel.
For the 1993 Lincoln Town Air Suspension, Page 00, click here.In this diagram, I see a #1 fuse 15A in the I/P fuse panel. Same as above! Plus a fuse #U 30A in the engine comp fuse box.
For the 1993 Lincoln Town Air Suspension, Page 01, click here.In this diagram, I see a #1 fuse 15A in the I/P fuse panel. Same as above! Plus a fuse #8 15A in the I/P fuse panel.
For the 1993 Lincoln Instrument Illumination, Page 00, click here.
In this diagram, I see a fuse #7 5A and a #11 20A both in the I/P fuse panel.
So, the fuses I see in common are the #1 fuse 15A in the I/P fuse panel which powers the Air Suspension and Trunk Lid Pull-down.