Any ideas?
First ohm out spark plug wires to see if rear wire is bad. If ok, swap the wires going to the primary of coil. Then swap secondary wires at coil tower. Start bike. If coil is bad, problem of weak spark will move to the front cylinder. If problem stays in rear cylinder, it's most likely a coil driving issue.
Would be helpful if you supplied model number or link of S&S coil and compufire ignition.
The compufire model is compufire 21835
S&S coil is S&S High-Output Single-Fire Coil - 55-1571