I am no expert, just putting my small amount of knowledge out.....
Manual Transmissions are coupled with a 4.3 rear end, while Automatic Transmissions are coupled with a 4.6 rear end. Also taking into account SE usually came with 31's (tire size) vs XE 235's (tire size). This affects the speedometer and odometer gearing in the transmission. Remember that we need to understand that each tire brand within the same size will give you a slightly different rotation distance to the measure of a mile (this is where the +/- error variation comes in). So if the conversion was an XE transmission with gearing for 235's and a SE automatic 4.6 rear end ..... these issues can really throw your numbers far off.
I am sorry this is all I can add to this conversation, I hope it helps. If not then please just ignore all my efforts. .