You're welcome :-)
Good to hear things went mostly okay. I'm not going to address everything you said, only parts and I'll leave the rest to others.
1. The disc order in very important, but in general remember that overlays are "like" patches. They aren't literally but they resolve that way logically. So you MUST put in the original base media for optional drivers, applications, and optional CDs FIRST. Then you "apply" the overlays. Otherwise the overlay's don't know what to overlay. I tell people to think of the media an entitlements. By putting in the original applications disk you show what applications you were entitled to, then the overlays know what to resolve to version update! So treat the overlays like an old windows service pack, you cannot update what not set to install. Easy to think of it that way.
2. Doing item 1 incorrectly leads to a very insidious problem, you can very easily (and inst won't warn or stop you) install a BASE program and never get the update (because you introduced them in the wrong order) and now you have crashes and application issues you cannot figure out! NFS is a prime example. For NFS you have to know the correct path for INST (you didn't, that's somewhat understandable). It's normally /CDROM/dist/dist6.5. That should have been your inst open path on the NFS CD, NOT /CDROM/dist. Now the issue, if you do the CD out of order (after the overlays) or just by itself Irix will have NO IDEA it's OLD and needed an upgrade, so you install an OLD application...thats has issues that no one else has because you effectively installed the 10+ year old version into the late-version OS.
Rule of thumb, introduce ORIGINAL CD, then introduce ALL overlays discs for your version, then hit done. Updates to drivers and original Irix content are in the overlays!! If you just put in an original disc...old gets installed. If you want the correct versions of things, you introduce ALL original/old software CDs, AND dev libs, and THEN insert overlays for final evaluation. That's the easiest way to get it all right. You cannot skip discs unless you know you never needed the content of that discs (new or old). You were 100% CORRECT to run BOTH applications discs..Old then NEW...that's the way.
3. Java and the other one always conflict, no one cares, removing them is correct, then it all works..you were correct in your install there as well. It's just a dumb thing when you do 100% of the OS instead of pick and choose.
4. I'm not going to go through full networking with you as it's been awhile so I'll let someone else do it. But for irix it's extremely important that...ethernet must be plugged into a LIVE network before PROM BOOT!! Else it complains and sometimes never seems to recover...don't ask me why...just put the cable in and make sure it's live before system startup. there is a needed NIS/DNS setup, even for DHCP, that you have to do, I forget what it is, someone will come along on that I'd think. It's a config file thing...DHCP doesn't work 100% in Irix like it should some info is static for some reason.
5. There is a support process called ESP that takes a TON of resources, SGI is gone...the process was part of their support system. Do a "chkconfig esp off", and get back a bunch of quickness for start and shutdown, at least.
https://software.majix.org/irix/admin-chkconfig.shtml
That's where I'm going to bow out, glad your fix was dirt simple for the found O2, I assumed you'd be dealing with dead CPU, so you got very lucky.
Have fun and don't be a stranger!
NEED -> 