Not fireing in rear cylinder

First a hello to everybody, as for I am a new member to Bike Talk! My first question is a big one! My 99 Sportster started life as an 883 and has been converted to a 1200 before I bought it, there has been extensive upgrades to this bike, and it has ran like a dream in till today! This day started as any other but it had a nasty backfire in the rear cylinder after warming up, I then shut it down and did a carb tune-up and checked the plugs. The plugs were very black and the carb tune-up proved to be worthless! Problem being now I start it up after and the rear cylinder is not firing AT ALL! PLEASE HELP ME, anything would be helpful!!!!

I would have to agree to check the to see if the plug is firing at all? simple way to do this is to take it out, place it on the head and turn the bike over. I am not sure that if it is the coil, because if the coil is bad, neither jug would fire. Make sure when you check for spark to rotate the plugs from wire to wire. This will tell you if the plug is bad or if it is wire or not. I had a similar issue with my 96 sportster probably with similar mods as yours.

Ya so I tuned thecarb up, did piss all! Well maybe a bit better? So Ichecked continuity throw the plugs and guess what Harley Davidson plugs cracked about halfway! I was going crazy thinking what the @&$ did I get myself into with this bike? Obviously jumping to the largest possiable problems first, but thank god a couple new plugs, dialed in the carb and a screamin down the road I went!!!
A big Thanks to the guys that responded!