This doesn't sound like a problem I've run into with any of my RZ's unfortunately. But does sound similar to a problem I'm currently having with my V6 truck. Please do let us know when you've figured it out.
The lack of a check engine code only rules out a hard ignition or injector related...
I'd look into a new OEM muffler and have a good exhaust shop mandrel bend all new piping at that price point. Or an aftermarket muffler if that's what you're after.
It's a local 99. Stellar Blue Pearl 3.4 5 speed. Was around 560k earlier this spring. Should be seeing it within the next few weeks. Guessing it'll be 570k or so now.
Update: Came in last week, sitting right at 570K and still in amazing condition.
There's surprisingly little that is exactly the same as your SR5 but there's a handful of stuff that's always in demand.
Headlights
Foglights
Center console and ebrake lever and mount
Tan steering wheel
Leather seats and door panels (inside door handles also are different)
Anything woodgrain...
They only used those through 99 or 2000. By 1999 only low end SR5 and the Highlander editions had that style the higher end SR5's with leather seats, sunroofs etc also came with the wide paint matched flares. By 2001 just about all of them had paint matched flares except base models.
3in Suspension Lift Kit for 1996-2002 Toyota 4wd 4Runner [77130] | Rough Country
I'd recommend planning on replacing front shocks too at some point. Either stock replacements or a lift strut like a bilstein 5100 to get rid of the spacers. Big performance difference, but anything new is better...
In the grand scheme a couple hundred for some springs won't kill you, but there are options out there.
For a 2 inch lift you can get away with either factory FJ Cruiser rear springs, or 5th gen TRD pro rear springs. You may get lucky and find a cheap pair on facebook.
Another good budget...
I don't have the answer for you, but the 99 cluster is completely different from the 98 cluster. You need to find info for 96-98 specifically to make it work.
First couple parts finds for this one ended up being partial. I've picked up a transmission and front diff, a little more expensive than expected at $500, but with sub-150k miles I found it hard to say no.
Then the local junkyard payed off just a little bit with about half a rear bumper in...
That panel is typically fairly easy to find especially if you're not concerned with cosmetic damage. Just make sure you get the right one if you're driving too far for it. They changed the color of the panels and size of the cubby in 99 and they do not all have the plug in.