Ok let me get this straight so i know where you are at...
You charged the battery, assuming it was low and the electric start wasn't working or?
Now it turns over with the electric start but the engine isn't firing correct?
You got a problem but its not due to charging the battery... And the fuses won't do jack as far as spark is concerned. These trikes have an AC ignition system, seems like we go over this about once a week lately. The ignition system and the battery charging/lighting/electric start system is two completely separate systems! The alternator/stator output to the rectifier/regulator charges the battery, runs the lights, and thats it. The ignition source coil and pulser provide the AC to the CDI and in turn the ignition coil and the spark plug. These systems have to connection to each whatsoever. The fuses are for the DC systems, lighting and electric start only.
If you need the service manual its available on my manuals website, link is below in my signature. Have a look at the wiring diagram.
Ok now lets start with what you can do! Pull the spark plug, ground the threads of the plug on the head and crank it over, do you see spark at the plug? If not then you have to start going through the ignition system. Check your kill switch and ignition switch, make sure neither of them are grounding the kill wire, a common problem is a faulty kill switch on the handlebars. Been there done that!
---------------------------------------------------------
1984 Honda ATC200ES "Big Red"
1982 ATC200E "Hondie"
1988 TRX300FW "Project Quad" Still in progress....