I've had a 350F daily rider for 25 years now, they are great little bikes. 500 miles in 10 years -- you need to ride this thing more! Letting the bike sit is worse than taking it for regular spins.
The 400F stock exhaust indeed fits and requires no rejetting, but you'd also have to change the pegs (with shift linkage), brake lever, and kicker (unless you rely on elec. start).
For the fork boots, IMHO the original fork ears (which had an upper and a lower, and were painted to match the side covers and tank) look way cooler. You can google image a photo to see what they look like.
In terms of the noise, have you done a 3k mile tune up -- points, plugs, carb sync, valve adjust? Hard to say what the noise is without hearing more, but out of sync carbs can make for some noise and rough running.
You should definitely keep the original brass from your carbs and only replace the rubber. Aftermarket stuff tends to be iffy, and this includes tune up kits with points and condensors. I think you'll find using oem for that kind of stuff is the consensus option here, but I can't speak to the spceific stuff you listed (although 4-1 has its fans).
Can't speak to the headlight conversion. I've considered it but never really had to (although if I do more night riding here in CDMX I might, as street lights are dim and sometimes non-existent).
I put a drop of oil on the round seal when rebuilding petcocks to help it move.
If you replace the gas cap rubber, make sure that the vent in the cap is open and functioning. If not, a new gasket will make a seal and fuel won't flow.
Dunno about the air box rubber, but if you need it, you need it. Getting the carbs and airbox off is a serious PITA with these, and takes some wiggling.
Dunno why you'd replace the coils if the originals are still working. They rarely go bad in my experience.
There are other otpions for exhaust as well, I'd go with Delkovic over Mac, but I'm not sure about centerstand compatability.
From the photo, you've got non-stock rear and front turn signals (the rear are obvious, the front have alonger stem than stock 350F).
I'm sure others may chime in as well.
These are great bikes. I rode home from work today and there is a stoplight just before a windy uphill section close to my house. It's fun to wind it up from dead stop, get in front of cars, and whip around the corners. And if you don't know already, these things love/need to be wound up, you won't get anywhere under 5k rpm but around 7k is where the fun is.
