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motor swap from hell!! Please HELP



I have a 1998 mustang gt with an automatic transmission  (4r70w), well a couple weeks about my transmission starting slipping really bad and i couldn't even get into 1st gear. well a guy locally had a 2003 mustang GT motor and transmission (4r70W) for about the same price it would be to get the 98' trans rebuilt. so i went for what i thought was the better deal and bought the 03' motor and transmission. i kept my 98' harness and used my 98' computer.  I got the motor swapped in the car and it fired up just beautiful but the problem is with the transmission.
on the left side of the transmission about midline there is a transmission speed sensor with a 2 wire plug on the end of it. but the connector from my 98' harness don't match and then on the tail shaft where my mechanical driven gear was on my 98' i plugged the plastic gear in the transmission and there was no gear to help drive it to make it turn.
now i understand the big differences between the 2 years and electronics and the speed sensors and signals, but im stuck!! i thought i had a solution which was to buy an 03' computer,dash harness, engine harness, and instrument cluster. and just swap it all out with my 98' and have some major things like the PAT system and  the fuel line return issue's corrected with a custom tune. but as the digger i looked for info i realized the fuse panel under the hood on the car are different as well!! like with the # of circuits in the panel on the 98' compared to the 03'. im very lost for words and trying to find a solution and any help would be appreciated and as well to put the icing on the cake, its my daily driver as well.


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