To the best of my knowledge, they're the same. The difference came in 2000, where they went from external balance to internal balance in 2001. I am not 100% positive of the actual dates of the changeover, so you may want to research it before buying an engine. Also right around 2001, they went to IMRC (intake manifold runner control) which used a completely different upper and lower intake, different cylinder heads, and different ECU and wiring. Same short block as the 6 port 3.8's but thats' where the similarity ended.
I am about 75% sure that the change from external balance to internal balance happened in mid 2000. Meaning, late 2000 models had internal balance and early 2000 and prior were all external.
Ironic that you mention replacing an engine. I've got an 04 with a 3.9 and considering finding a good JY engine. Mine runs good but it vibrates and its getting worse. At 315,000 miles it's probably getting close to time anyway.
'92GT, 427" and '93 "LXVO" coupe