GM changed the separator plate somewhere around there or a little bit after 99.
Its been a while since i had one apart, but i remember in the early 2000's GM had a new part number that supposedly superceded the old plate in the early LS cars and was supposed to do the job, yet it wasnt right on some of the valve body passages, there was barely enough overlap.
Some passages in the vb had minor changes.
The newer pn plate was ok for the newer vb , but didnt sit right with me being used on the old vb, despite it coming up in GM's shit as the right part for the job.
Anyway I never ended up using the new separator plate for this reason. Im sure some could miss it though.
Im not saying it is this but if you can find out if the separator plate was changed, and perhaps if you cant solve this externally or someone else can chime in with an idea, you might want to pull the vb at least and check the separator plate fit, and the other things people already mentioned.