Side gapping is a style of gap, not necessarily distance of gap.
There are two ways of doing it: one is called "tee gapping" and the other is my favorite, "side gapping".
The former involves shortening the ground electrode so that its end stops right over the middle of the center electrode, when viewing it straight down from the bottom.
The latter, side gapping, is the cutting short of the side electrode so that the complete center electrode is visible when you look straight down at the bottom of the plug.
I use wire nippers/side cutters to shorten the ground electrode. You normally have to bend that electrode up to be able to clip it. Then, I take a points file (remember those?) and dress the distorted end where I clipped. Make it look like the original end.
The downside to these mods is that they shorten the life of your sparkplugs. BUT, plugs last so much longer now that I don't think it's an issue of importance.
OK, here's the answer to your question: I regap the plug to whatever gap I want. In the case of a stock Bonny ignition system, go with .035". You'll have to put your feeler gauge in on about a 45* angle to get a propper reading on a side gap, but a straight-in-from-the-side measurment is what to use on a tee gap (since the side electrode end is hanging half over the center electrode).
Yes, these bike ignitions need some help in the form of a higher output spark box. The 360* standard firing Bonny, T100 and Thruxton engine is easier to do than the Speedy and America, but someone who is well versed in automotive igntion systems could do it. No doubt MSD in El Paso, TX could make a box, but I don't think the market is big enough, and the box would probably be fairly expensive.
The main reason one would want a "hotter" electronic ign. box is that he could then widen the spark gap to something serious, like .065". That bigger gap gets the flame front going better. Think of it as starting a bonfire with a plummer's blow torch (another "remember those"?) as opposed to a matchstick.
