I have a 1991 Samurai with a 1.3 liter throttle body setup.  
I just got it started after a few years of sitting and the engine knocks something terrible.
Loud metallic sounds coming from the crankcase, ouch.  
I have a number of options, I could:
1) rebuild the existing engine, likely replacing the crankshaft, some rods, pistons, rings, rebuild head, etc.
2) rebuild a 1998 short block that I have and use the 1991 head after it is rebuilt.
3) rebuild and install a 1.6 engine I have from a decent running 1998 Sidekick.
My concern is the 1.6 Sidekick engine was out of an automatic.
I am not sure if the ECM that I have from the Sidekick with an automatic will work with the 5 speed in my 1991 Samurai.

I was also told I could use the 1.6 bottom end and the 1.3 top end together, but I am not sure because the 1.3 is a 8 valve, and the 1.6 is a 16 valve.

I would like the power steering function from the 1.6 setup.
It seems the cost of rebuilding option 2 or 3 is going to be fairly close.
Option 3 will require some kind of adaptor, I think.
Option 1 will require more parts than option 2...
What's your take?....and thank you...!

The early 1.6L's were 8valve engines and would fit under the 1.3 head, but the 16v version requires either a 16v head or rebuilding with 8 valve pistons to use the 8v head. You should be able to find a manual trans 16v ECU fairly cheap. 

The early 1.6L's were 8valve engines and would fit under the 1.3 head, but the 16v version requires either a 16v head or rebuilding with 8 valve pistons to use the 8v head. You should be able to find a manual trans 16v ECU fairly cheap. 

I was once told that the auto trans ECU from a 1.6 - 16v will work with a 1.3 - 5 speed but, the ECU from a 5 speed 1.6 - 16v with will not will work with a 1.3 - 5 speed. 
I have no idea if this is accurate information.

The auto ECU's will not work with a manual trans without throwing codes, the manual trans 16v ECU will work with the 1.3 manual trans, that is the normal route taken and what is used by several companies that do swaps and make products to swap the 16V into the sammi.

On the other hand, if you simply rebuild the 1.3 then you don't have to worry about what fits with what and compatibility issues.  If you just want it to work, I say rebuild the 1.3.

Xoloski,   Any chnce that the ecu from the 98 auto is 2wd Wanna sell it ??