With coil wires reversed you have spark around bdc on intake (intake valve almost closed) and powerstoke (exhaust valve just opening) - it can "backfire" either through the exhaust or carb.
I suspect we've all done this if we've dismantled a few engines. Not a big deal, like anything else we learn best from mistakes.
If that's not it, backfiring can be from poorly sealing valves - burnt or misadjusted. Or really badly set ignition timing.
I have given up on ever getting a seep-free 400F head-barrels joint. It's just a bad design IMO. There's so little space between the orifice valve and the outer edge. After multiple gasket replacements, head and barrel planing, different gasket sealants, different orifice valve seals... I just accept it will leak, and jam a wad of paper towel between the fins to soak it up and replace the wad when saturated. One can find paper towels or restaurant napkins just about anywhere.
An external oil line system with the orifice holes blocked would be nice... but the head mods are outside the limits of my skills and schedule.
Jetting the 400 for pods, MC-Again's or anyone else's, is a major pain. It can be done well (others will insist it's not possible) but you have to be systematic and have a lot of time to devote to the process. To me, 95 mains sounds too big for a stock engine regardless of pods or exhaust. The biggest I've used is 92, as I recall - with a 466 kit, pods, hot street cam, and headers.
Set up your valve lash and ignition timing, then do a full throttle plug chop. With the right mains (tan plugs at full zot) and the idle screw optimized... the midrange will probably stink - surging and hesitating regardelss of needle clip position. Since changing the slide cutout size is not really an option, you have to modify the needle profile to get the engine tractable and responsive at all RPM/throttle combinations (within reason - it will always die if you crank full throttle at idle).
Admittedly even with really good carb setups the engine will act weird with pods (missing, surging) in some rareish conditions of bike speed and sidewinds. Sucking air from the bizarro turbulent flow area behind the heads is not ideal. But I still love pods for the sound and look. Plus I keep spare plugs etc in the otherwise empty airbox.
