First, even though 6.0 is the latest version, I would for now stick with 5.1.3 (latest of the 5.1 code train). 6.0 just came out recently with the new 5600 line of switches, and unless you are stacking with one of these, or require some of the PIM multicast routing, I'd stay with going to 5.1.3 switches.
Since 4.1 is fairly old code, Nortel states that you will need to at least step through 5.0.0 before going to 5.1.3 to eliminate corrupting the configuration. Also, at some point you will need to set the base switch on the unit that will become the base of the stack; this switch is only read at boot, so you might as well turn it on when you upgrade the firmware.
With this unit set as base, and if you step through the upgrade, the configuration will stay on the base unit. Also, to be safe, I have also made sure that the new switch code matched what I was going to. I've also been able to have the new switch go through automatic code updates, but the secret here is waiting; it will take 5 minutes or so for this to occur.
I've done this before and have pretty much been successful with the following:
1. Flip the Base Unit switch on on your production switch.
2. Upgrade to 5.0.0
3. Upgrade to 5.1.3
4. Stack the switches together
5. Wait for the new switch to join and upgrade code.
You will want to back up your configuration as a ASCII rather than Binary prior to the work.
