Michael,
I also have an SS elan. I originally ordered an S4 wiring harness thinking it would work.....not. This was done about 10 years ago now. Working with the original S1, S2 wiring diagram and with British Wiring, we came to the conclusion that the S2 wiring harness would do the trick. Difference on the S4 harness was spade connectors where there should have been bullets, alternator wire instead of generator. If I remember correctly, the brake fail switch and warning light needed a wire added to the S2 harness and also a warning flasher needed to be added. So I purchased some wire to match the existing wiring and just wrapped the new wires into the new harness as needed(bought harness tape from B.W. ). Also window switches to door motors have small separate harnesses. You may want to review the additions to your car for the SS modifications and compare them to the S2, S3 wiring diagram. Buy a crimp tool, bullet kit and replace all the old connectors. Check your fuse block for connectivity and tightness of rivets in the spades. Confirm your voltage regulator is working correctly, otherwise poor connections especially with the main power supply will cause charging problems....took me years to find this out. While you are under the dash, replace the headlamp relay as cheap insurance since it's so hard to get to. I ordered a POWER PROBE
https://www.amazon.com/Power-Probe-III- ... 335&sr=1-2 to test everything as you can connect to the battery and either ground or power a circuit via the probe. Use an inline short detector
https://www.amazon.com/GearWrench-2524D ... ve&sr=1-61 like the round barrel one or similar. These have a bimetallic breaker which resets itself almost immediately thus no damage to any electrical.
PM me if you have more questions and I will try to help.
Greg