Will an '01 HO ECM work on my SO 99?

Only if its reflashed with 99 software.

Are the engines that much different?

Not that the engine is different as it is the engine controls and sensors change with epa changes for emissions and the way it comunicates with the pcm changes with tranny and chassis changes from year to year. It is a simple 10-15 minute flash at the dealer but they will charge you an hour flat rate fee.

Not that the engine is different as it is the engine controls and sensors change with epa changes for emissions and the way it comunicates with the pcm changes with tranny and chassis changes from year to year. It is a simple 10-15 minute flash at the dealer but they will charge you an hour flat rate fee.

Like you got federal emissions, California emissions, Canadian emissions, automatic transmission, manual transmission, SO vs. HO software, etc. I heard there is like 40 to 50 different versions of software.