The rear brake problem is likely related to fouled brake pads. I'd change the disk and the pads and see if that does it. You don't want a solid rotor in California anyway. While you're at it, bleed the system and get some fresh DOT in there. That solid rotor has likely sent some serious heat into the system.
The Messico pipe is the stock pipe from that era. It was fine. Unless it's damaged, I'd run it. I've heard that they are delicate, but I've had two different bikes with it on there and can't remember ever damaging, or even denting one. The FMF is probably the most common, least expensive replacement, but frankly I don't think it matters much. The old Doma was very nice, but very expensive. That Messico should be great, put it out of your mind unless it needs to be replaced because of damage.
Sag: Lots of guys run 110mm of sag on the older Gassers because the rear was a tad high. A set of LTR pull rods puts it in the right spot so you can run 100mm.
Oil: No filter, correct, it's just transmission oil, no real need for a filter. A two stroke gets all it's engine lubrication from that 32:1 fuel/oil ratio. The transmission takes about 1 quart. You can overfill most any two stroke transmission by 25% and be fine. I frankly don't know the capacity, but I've been dumping an entire quart in the tranny of each of my gassers since 1999. The sight glass is just there to make sure you have oil, and look at it's condition. I don't think it's a level, at least I think someone once said that, perhaps the dealer I first bought my initial bike from. Don't know. Just dump a quart in. Do yourself a favor and get a tiny funnel, or a hose into the bottom of a funnel to fill your oil. The single biggest flaw of all Gas Gas bikes is that stupid tiny little oil filler.
Kicker seal: Easy fix. Drain coolant. Take the kicker and brake pedal off. Lay the bike on it's left side. Remove radiator hose to water pump. Use 5mm allen wrench on a socket or speed wrench and pull all of the screws out of the outside of the clutch cover. Not the little clutch cover, but the case half sized clutch cover. Remove the side cover and poke the seal out. Press new seal in and reverse process. Don't forget about your return spring on the brake pedal, or the coolant in the radiators.