Mine had the plastic boxes and builtin amps but it wasn't the upscale radio. Back in '90 I was stretching it to buy the cheapest 4WD 4Runner I could. The only thing I added on was the A/C. The sales manager hated me, they make their $$$ on options. The salesman threw in a leather shift knob.
I put in 5.5 inch speakers in the rear. If you can fit in 6.5 inch you'll be better off, they really do sound much better, as I have since found out.
Everything I've read seems to indicate that oval speakers suck, rounds are the only way to go.
I recently put tweeters in the top parts of the kick panels and a powered sub under the drivers seat.