18 hp b&s problem

Hey guys I have a MTD GT1846 with the 18 hp opposed twin briggs & stratton engine. I'll start at the beginning of the story so you get an idea. A while back when this lawn mower had the muffler on it, it was having some power troubles. Half the time it was only running on one cylinder (later found out it was the right cylinder) When I rev'd it up from just about any idle, it would only idle up on one cylinder then eventually the other one would kick in. When you engaged the mower, like any other lawn mower, it bogged down a bit but of course came back up to high idle with one cylinder firing then soon the other. So any time the engine would get bogged down some how, it would only run on that one cylinder. So a month or 2 ago, I decided to take the muffler off and put custom pipes on it so i could 1. Find which cylinder it was and 2. Because I didn't use the mower much so wanted it to sound "unique" So sure enough it was the right cylinder not firing half the time. I cleaned the spark plugs up and it was a little better. But when i was mowing last night, the spark plug wire on the left side (the side that ran OK) popped off and it was running on only the right cylinder and the pipe on the right side (i put duals on it), which was the only cylinder running, was shooting out flames like crazy. Pretty much every time it fired it shot out a flame. But it did not do this when i left the left wire plugged in and unplugged the right one. It shot no flames whatsoever. So it is the right side cylinder is the one with all the problems. Sorry for the long story but does anyone have an idea of what it might be? Any help would be appreciated. Thanks!