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There are 2 99 models- an early 99 and a late 99, or 99.5. The early model has a smaller turbo, smaller injectors, different HPOP, and some differences in the front end (brakes and track bar mostly). The late models are more favored by the go-fast crowd because parts are more readily available.
99.5-01 no real big changes. Some of the 01's got a diode in the trans that was failure prone.
Somewhere around 01 the rods in the motor changed from forged to powdered metal (PMR's). The PMR's aren't as strong as the prior forged rods and things get a little dicey once you start pushing the 400hp mark. PMR's like to try and escape through the block once you get into that range of power.
02-03 saw no changes to the drivetrain but got some interior upgrades- different gauge cluster, slightly different dash, more little stuff.
That's it in a nutshell, hope this helps.
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