i can get a 98 Taco 4x4 MT ECU for $175, and I have located a 96 4runner 5VZE for under $1000 with only 60,000 miles. Will these two match up?

 

If the ECM was for a 5speed, probably.
I believe if you take the engine ser # to the dealer, they can give you a number for the ECU that will work.

 

Here's another question. I just found out the Engine I've located is out of an auto. Is that going to be a problem? I'd get an ECU from a manual and I'm putting it in a manual truck.

 

Check out this place for listings of factory ecus and numbers:
http://www.ecudirect.com/finditfast/
From my quick check, they do not match up.
And a very important bit stolen from Offroadsolutions.com:

"If your vehicle has a 3VZ-E engine, this kit allows the use of your factory transmission. The R150 (manual) transmission is nearly identical to the unit placed behind a 5VZ-FE from the factory. If you are using a manual transmission, the 3.4L engine needs to come from a manual transmission vehicle. In SELECT year models we have found a difference in crankshaft machining from the factory. In these instances an engine from an automatic transmission application will not accept a pilot bearing. Another reason to purchase a manual transmission "package" is the difference in electronics. The engine ECU and the engine wiring harness are completely different manual to auto. Based off experience, we recommend purchasing all the used parts from the same manual transmission vehicle. Once again, purchasing all used parts from the same donor vehicle has been proven to prevent grouchy mood swings."

 

Well that completely sucks! I find an amazing deal on an engine and I can't use it! So... Now I guess I'll start calling up the local insurance agencies to see if any has a newer vehicle that is going to be totalled soon. Try and get the engine before it hits the junk yard.

 

Another thing to consider on such an early 3.4l engine is that they had the same headgasket problems in '96 and '97 on the 3.4ls that they had all along with the 3.0s. I believe I even came across a similar headgasket "service campaign" for them as the 3.0 had when I researching putting in a 3.4l. I finally decided to just not do a 3.4l and someday hopefully do a 7mge swap. Of course, this also had headgasket issues (sensing a trend here), but the apparent consensus on various Supra sites is if the gasket hasn't already gone bad, you can just crank up the factory bolts to 72ftlbs with considerable success.

 

Well, I wouldn't worry about the HG on this engine. The 4runner it came out of is owned by a professional mechanic. I guess he got a really good deal on a 2002 engine and decided to swap.

 

"..has been proven to prevent grouchy mood swings."

Good stuff!