The engine will remain stock since I figure I will gain a little power by reduction of stock parts and possibly by adding some air filter pods.
Good - internal mods on a 400 don't really make sense to me. Do your research before going to pods, though - they can make the bike very difficult to tune.
Since it is light and nimble, it will be an ideal bike for the type of riding I like to do which is canyon carving, so any performance additions will be
I'd say it'll be a workable bike for that type of riding. Anything with sporting pretensions built in the last 20 years would work better (although not necessarily be more fun).
clip-ons, tapered head bearings, rear sets, master cylinder/brake caliper rebuild, drilled rotor, stainless brake lines,
Those all sound like excellent ideas. Along with the tapered head bearings, you probably want to look at swingarm bushing refresh. And to complement the brake work you're planning, look into some nice brake pads, too - I've liked EBC HH pads on my other bikes, but don't know the common wisdom for good pads on a CB.
and the cb550F fork swap to name a few.
I don't know anything about the CB400 forks, but the CB550 ones are not particularly good stock. Race Tech sells their cartridge emulators and springs for both the 400 and 550 - your 400 forks with the right springs, the RTCE's, and a good brace will work better than a stock 550 fork.
That work done to the front plus some genuinely good shocks in the rear will make a bigger difference to your bike's manners, comfort, and safety than any other mod you can do.
If you're going to have the bike all apart and do brake and suspension upgrades, then consider some bracing of the frame and maybe the swinger, too.
With that being said, is there any place I should start first or do I just have at it and start the disassembling process? This is a project I will be getting into blindly so any information along the way would be great since this will be a learning process start to finish.
Plan your work, and work your plan. Since you have a road-legal runner right now, break your plan down into phases, doing the easy stuff first. Try to break it up into small 2-to-4 week chunks and ride it in between mod sessions. Take a systematic and orderly approach, and figure that everything you do will take at least twice as long as you expect - and probably have to be revisited afterward at least once to correct some mistake.
And most importantly, POST PICS!!!
