Here's one I did for someone not too long ago, it's a CB360.
Aluminum plate was made in a break, 360's have a bolt on rear hoop, so the holes for that were utilized to bolt the plate on, and the hoop was flipped and welded before powdercoat (see the turnsignal brackets pointing up? Also, his decision, not mine.)
That's a ballistic evo2 4 cell battery. Runs the electric start, but only until it gets cold out. Otherwise it's a good battery for the size- 8Ah (lead equivalent) so it can actually handle the charging system for extended periods, but it's probably not good for long trips. They make bigger batteries, though.
This is what covers up the panel- it bolts on from below.
And, for what it's worth, a smaller tail would still fit over this electric panel- all that stuff would fit under the tail on that 550 you posted as "inspiration."
Regarding the splash guard, you can see clearly that this one doesn't have one, but I wouldn't recommend it, for all the reasons you are already thinking about. Clean up the stock plastic, paint it, or whatever, but I'd keep it around if you plan on riding the thing in varied weather. Leaving it out will just cover the carbs and the back of the engine in grime- shorter air filter life, potential of stalling it out in the rain when water from the tire soaks the filters, etc. Show bikes are sweet and all, but they're full of big compromises in the name of vanity.
Also, I just looked at the pics of your bike, and you know you have a 1977-1982 750 comstar front end there, right? Just FYI for when you start sourcing parts. A stock 750k wheel can probably be made to fit correctly, but keep in mind that the caliper mounts are different, and so are the rotor sizes between the two styles.
