V6 Replace Engine/Engine Fitment Question

[jimjim5 0]

Hello, 

My 2000 V6, with a manual tranny needs an engine replacement. Looking local and online, and it seems as though I have a narrow option for engines that are direct fit/plug and play for my year car. (For instance, when I search for engines for my 2000, the only options are 1999-98 engines, and the results are more narrow if I search by VIN. However,  if I search for 2001 or 2002 engines I get more of a selection.)  It has me VERY confused! I would logically think any motor from 98-2002 would fit without issue?! 

Does anyone know why these different year engines are not interchangeable (low emissions vs. federal, manual vs. automatic, harnesses, etc...)? Does any of this make sense? 

I have searched the forum, but the information provided is not absolute. 

Any help would be appreciated, as I don't want to make a mistake purchasing the wrong engine.