So I got a 94 Suzuki sidekick 4door 1.6 16v 5speed 4x4 the other day with a blown head gasket. Pulled the head and it was badly warped. Bought a supposably running 1.6 16v. Got it home and did the timing belt, water pump and oil pan gasket. I noticed son differences in the intakes and oil pan gasket.

The oil pan has a crank position sensor I believe. But I do not have a connector on my sidekick for it. Is this a problem. I believe the engine is a 96+ because of this oil pan configuration.

The intakes seem to be the most different pieces I can find. The newer one has two plugs that in guessing are emission related because they are on the back/passenger of the intake and are hooked to vacuum lines. I do not have connectors for these as my old intake did not have them. Is this a problem?  The distrutors seemed different so I swapped my old one in because the wire connection were different. 

I had a friend help me pull the original engine and he took off three wires from the back and I have no idea where they go. They all have ring connectors so I figured grounds. I grounded all three to the block and have a major short when I hook up the battery. It blows the 60a fuse after the battery. The colors of the wire are. Two wires go into one ring connector and they are blue with black strip and black w green. There are two other single wires to ring connectors and I believe they are both all black. Any idea where these go. 

I also snapped off a water temp gauge in the intake the one right above the green connector by the thermostat. I believe it's ac related but not positive.

Should I just switch intakes and use my old one? 

Partially speculation here...but I am guessing the differences are obd1 and obd2.  The newer motor is gonna be obd2, so there are some different things required for the computer to work.  Swapping to your OBD1 intake and distributor is going to be your best and easiest route.
How badly warped was the head?  I know from experience you can shave .030 off the head and still use it.  And it sure improves the power.

Ok should've thought about the chances for different 16v. New to Suzuki stuff. Ok next question will I be able to use my intake on the newer head?

Once again, somewhat speculation, but I think so.  Check for a difference in the part number for the intake gasket.  Most of the experience I am drawing from here is Honda motor swaps and mixing OBD generations there.