I had a '93 Explorer. They only came with a 4.0L and an automatic. IMHO the transmission was junk. This was the same time period Ford had the AEOD in the F-250's and that transmission was a 60k mile transmission at best. They went through a period there where all the Ford tranny guys must have retired and the kids straight out of college couldn't find their @$$ with both hands. And my Explorer got a lifetime average about 16 mpg (I kept track of every gallon of gas that I put in that vehicle so that is an average you can bank on). Now I don't drive like the little ol' lady from Pasadena but there is no way someone is going to get 30%-50% better mileage out of that vehicle.
That's actually not correct...
A stickshift (M5OD) was available all the way up through at least '00 or '01 Explorers ('03 for Sport models). As you get later thru the years though, they do become harder to find (if I was to guess, I'd say less than 5% of '00 4-doors and less than 10% of '00 Sports were sold with a stickshift, and most people tend to hang on to sticks of any year).
And on the automatic (A4LD), I strongly suspect the issues sometimes seen on them was not so much a problem with the tranny itself as it was with the weak factory cooling for it. A friend of mine put an external (aftermarket) aux cooler on his and he had about 230K on it when he sold the rig (and that was with having towed his boat a number of times too). I've seen others report good use out of theirs with an external cooler too. Whether the AOD-E or others would benefit similarly though, I can't say.
This is all pretty much moot though because the OP said he wants the stick.
As for "roost rulers"...
Something probably should be said of the fact there are a great many people out there swapping Explorer axles into Jeeps (which that alone I think says something). The Explorer also has a frame under it (anyone who's tried to open a door on a XJ while it's suspension is crossed up offroad should be well aware of the dilemma that would bring). I don't think I have to say how much more comfortable an Explorer is to drive too...
Tacomas actually do have quite a bit going for them (their pricing issues aside), though the A-arm IFS could limit it in some terrain more than the TTB setup on a 1st-gen Ex would (not sure what the OP's goals are here). But the frame rust thing... That did slip my mind when I posted earlier lol.
I do fully agree with trying to find a vehicle from say, Ca or Az though. No doubt, this should get you something in far better condition than what you're likely to find locally in a salt state. Like everywhere else though, people out here also think Toyotas are gold or some crazy isht, so don't hope for many deals out here either.
If anyone wants to brush up further on the Explorer (and the Ranger or Bronco II for that matter), there are excellent web sites out there such as
www.explorer4x4.com and
www.therangerstation.com. The people who build these rigs into wheelers are the ones who know them best, and which years are best to look for.