Rear cylinder does not fire 1987 FLHTC

Carb or fuel injection? Spark or no spark? Check for spark by putting a new plug into lead and laying on cylinder head. Leave old plug in engine. Start bike. If carb and no spark then plug or coil would be first suspects, then ignition module, then wiring from coil to ignition module. This is assuming you have compression on rear cylinder and all mechanical checks completed. If fuel injection and good spark, then ECU most common problem. Then injector, then wiring. If no spark, check coil, then wiring frpm coil to ECU, then ECU.

replace the coil and wires, check plugs for proper gap

The spark plug on the rear cylinder isn't firing. Check the plug for fouling and make sure the spark plug wire is good and connected to the coil and plug properly. Also check the spark plug gap (0.040)

try switching the position of the two coils, the plug wires will unscrew off of the coils and that way you dont have to pull the spark plug wires too,(be sure and change the 2 wire couplers too) if your front cylinder stops firing you know its the coil, if the back cylinder still doesn't fire then your coil is good and you either have a bad #2 spark unit or a bad crank pulse generator.

From standing in front of car and facing engine:

3.1L and 3.4L OHV V-6: The cylinder location is from left to right (rear cylinders) 1,3,5
(front cylinders)2,4,6

The coil terminals from left to right: 5,2,3,6,4,1
Firing order 1,2,3,4,5,6

3.4L DOHC V-6: The cylinder location is from left to right (rear) 1,3,5 (front) 2,4,6
The coil terminals are from front to rear 5,2,3,6,4,1
The firing order 1,2,3,4,5,6

3.8L V-6 cylinders left to right (rear)2,4,6 (front) 1,3,5
coil terminals front to rear 1,4,5,2,3,6
firing order 1,6,5,4,3,2

With a single fire ignition, you cannot swap the wires. A dual fire ignition, yes, but not a single fire. You need two things to get the cylinders to fire, spark and compression. Take the plugs out of both cylinders. Run a compression test on the rear cylinder. You need at least 100 PSI to get the cylinder to fire like it should.

Next, put your plugs in the wires, (they should already be in the wiresand grounded) and spin the engine over. Watch for the plugs to spark,especially the rear plug. If you have spark and compression it should run on the rear cylinder. If it still doesn't run, either something is way wrong with the ignition or a very bad air leak on the intake.

If you don't have spark at the rear plug, you need to check the coil. A single fire coil is different from a dual fire coil. The primary wiring is different as well. If you've got the primary wired incorrectly, you won't get spark at the rear plug. Go to the website of the manufacturer of your ignition system. Most of them have downloadable installation instructions. Check your primary wiring.

The first thing I would do is replace the spark plugs again. You can foul a plug and it will cause you more problems than you can ever imagine. I see you have done all the logical things that I would recommend but I did not see you have replaced the plugs after the 200 miles. You would be surprised at how many times a $2.00 part can cause fits beyond belief.