Some electrical info for you.
The ignition coils draws about 30 watts (stock 550 types)
The alternator draws 30 watts (to make a magnetic field so the stator can make power).
Fuel pump draws some power.
Tail light will have a watt rating.
Headlights will have a watt rating.
Instrument bulbs will have a watt rating.
Stop light will have a watt rating.
Etc.
They all add up to draw power from either battery or alternator output.
The electric start only draws power when engaged (about 120 amps, or 1500 watts).
While the muffler CAN effect the carb jetting, it is usually of secondary concern after the air filter.
The stock jetting was set based on assumptions of what restriction there is to the breathing of the engine. Generally speaking, if you change the breathing ability of the engine, the carbs cannot automatically adjust. So, they have to be retuned for the breathing changes made. Pilot screw setting, slide needle height, and even main jet size may need to be changed to co-ordinate with breathing changes made from stock. (particularly, those Pod type filters.)
I think you should figure out/finalize the exhaust issues first, and then address the carb jetting.
Unless you have a dyno, you will likely have to learn how to read the spark plug deposits to learn combustion conditions and then adjust fuel mixtures to obtain the proper color deposits.
What do you figure the top speed will be for that bike? Any info on final drive ratio?
I think I'd be too scared to ride that thing very fast. Don't they tip over if you brake in turns? I don't think I've ridden a trike since 1958-ish.
