Holy crap. You have serious issues.
NDS Manager is not reliable in this case because it's only looking at one replica. You need to see the status from all servers, which you do at the server level.
Just as a word of caution, you are in seriously bad shape and you could completely destroy your NDS if you do the wrong things here. You need help. Unfortunately Novell does not support NetWare 6.0 anymore.
654 errors mean that a partition operation never completed. The root partition wont' come on till this error has cleared. There are other reasons why the operation never finished, so the 654 is only a symptom of a much deeper problem.
DSTRACE doesn't fix anything, it just shows you exactly what DS is doing. Those errors are insane. You need professional help.
My company can help you, but don't think that I'm trying to solicit your business. It is just that it sounds like you are in over your head here. A lot of customers let it go too long, and damage the system severely before they call us. If they had called us first, they could avoid this and avoided a lot of pain and agony. Sometimes it costs 2-3 times as much to fix a problem that could have been a quick fix.
One critical thing - make sure DSREPAIR shows that Time is in sync on all servers. Do this from the Master replica of [root]. That is the #1 priority for NDS. If you get that fixed, well, its a start at least.
Marvin Huffaker, MCNE