I kinda agree, plugs shouldn't be bad at 36k. But you're having problems, so removing the plugs to look at their condition isn't a bad idea. Plugs say a lot about how an engine's running. And their not THAT expensive to replace, either.

Sounds like you have DI, so there aren't any wires. But maybe(?) take the coilpacs off & clean them? Put some sparkplug-boot grease on them? (Is that OK to use on DI???)

My '98 doesn't have a normal fuel filter either. There's a screen in the tank, kinda looks like a bag aound the inlet. It's not a routine replacement like the filter on my '95 Integra...

The rest of your description sounds like transmission problems. Is there a cable from your throttle to the transmission? (I don't know which years have that.) Maybe it needs to be adjusted so your transmission 'knows' your throttle position? But I'm guessing that in 2000 that's done electronically.

If the dealer says brown transmission fluid is OK, I'd take a hike. To another dealer. Or you could open a new bottle & show it to them... Honda USA has a customer service phone ## somewhere. They might be interested to learn which dealers are telling stories like that.