I have a 88 Samurai that i swapped a 94 1.6, 16V in to with a modded harness and the 1.6 ECU.
I would like to install an automatic trans, is there a difference in ECU
 programs from stick to auto?
What is the best trans to install?
I am looking at the 4 speed Suzuki trans.

As far as I know the 4 speed auto is electronically shifted, so there will be a transmission controller, and that, again, as far as I know, does communicate with the ECU (something related to throttle position) so I would expect the ECU to be different.

Thanks for the input.
yes the 4 speed is electronically controlled but i wasn't sure if there is a transmission controller or not.
I was hoping someone had done this before and could give a little insight into what I could expect to encounter doing this.
The 3 speed is not electronically controlled but then there is no overdrive for the highway.

There is supposedly a Volvo version of that four speed that has no electronics - the Suzuki transmission is the 03-72LE, the Volvo will be an 03-72.

Depending on your reasons for wanting to go with an automatic you should also be able to run the 03-72LE with a manual shifter - it would be like a standard transmission but without a clutch - research the AW4 as used on the Jeeps, and RADesigns shifters - the transmissions are very similar.

Thanks