As #1 above, all good stuff.
I'd swap out the intake rubber for a piece of 1 1/4" diameter x 1 3/8" long fiber reinforced radiator hose. It is stiffer for better carb support and has a VERY low rot-off rate. The OEM carbs have given reliable service, I've no real reason to swap them out. The Hitchcock's jetting chart is a nice guide, and internal tuning parts are plentiful.
I went to the Hitchcock's "Methanol alcohol" fuel tap feeding into a 10 micron filter. Always plenty of flow & no more dust & crud in the float bowl. Clean is good.
I like points, no voodoo troubleshooting and they work fine. That said, get the point advance mechanism extraction tool to make your life easier. Get a second set of advance springs and make sure your springs are properly tensioned and not sacked out.
After having a low load, gradual uphill soft seizure on the stock Velveeta piston, casi iron rings and iron barrel, I went to an alloy barrel and forged piston. Better sealing (steel rings!
) eliminated oil tank foaming (Nivea Syndrome) and a tougher piston and better heat transfer makes uphills a worry-free experience. Kinda modern even. The alloy barrel IS noisier though.
The OEM reg/recs on all my machines parked at a battery-killing 16V. The Boyer Power Box tames that to a steady & agreeable 14V. It also allows for kickstarting with a dead battery. Plan "B" for a kickstart machine is to keep the OEM reg/rec and use a 18V NiMH tool battery. The reg/rec can't kill them and they are small and idiot proof.
As a newer AC lighting machine, there's not much point to not just letting the headlight run continuously. A warm lamp filament is more flexible and you want maximum traffic visibility anyway. Once you aren't worried about on/off issues, a simple hi/lo switch takes care of business if you want to go back to Old Skool switches. Besides, with the 2004 you have the current (and available!) Minda switches. Mine have proven reasonably trouble free.
As Stinkwheel says, the frame earth/ground connection is prone to corrosion. Some attention and "love" to this connection is in order. Clean bare metal to metal, lightly greased, no paint or corrosion products. Maybe run your own "bonding" jumper to the casquette.
Rewiring is an interesting but time consuming project. From an electrician and Japanese bike owner perspective the OEM wiring is pretty awful. As a 2004 machine I assume you have electric start? There's a lot to clean up there that was grafted on by lawyers. As there aren't any actual "big loads", the small wire is actually OK. It's just the in-the-loom soldered (hopefully...) connections that need checking, as well as the myriad plug-in connections that often need cleaning & a bit of grease. Most of my wiring problems show up at the bit of loom that turns with the casquette.
Control cables have been an issue. I finally gave up on OEM cables and just use the Hitchcock's heavy duty items.
Clutch plates seem to like ATF best. My 500 came with a primary full of brown mystery motor oil which slipped disconcertingly until thoroughly warm. I finally went to the Barnettes friction plates and that seemed to end all the slippage. My 350 is easier to satisfy, ATF & OEM clutch bits have worked OK.
On the rear wheel, check the sprocket carrier "3rd bearing". They are in a high grit area and are an "open" bearing. Many here feel they are good for about 10,000 miles or so. Maybe a good place for a sealed bearing.
Good hunting - ACR -