You're offering me a free therapy session? great!
Replaced the transmission a few years ago, it's been working great but I suspect one of the bearings is toast, possibly on the input shaft. It's making a lot of noise in neutral when the clutch is engaged.
As for the engine, I tore it down shortly after buying the car (14 years ago). The only major wear I found was the pistons and timing chain components, I replaced those and rebuilt the head. Motor was tight and relatively trouble free up until a few years back. Long story short it's burning a lot of oil again, ticking relentlessly and combustion chambers are filthy.
It's getting too late in the year to wrench on it. Picked up a brand new Tacoma to keep me happily motoring in the meantime. Tossing between the option of A: rebuilding the motor on my own with a lower mileage block (this could take years) or B: Throwing both the motor and transmission in the back of the truck and driving down to Metric Mechanic. or finally C: getting out of the game completely as the car needs body work as well.
Poll