The hint is just making things more confusing:

Being familiar with the longest version of Gotta Jibboo that Phish has played to date can help you determine which year this week's MJM comes from. Be warned, however -- this hint is not as straightforward as you might think it is.

Ok, so we know 7/4/00 was the longest version of Jibboo by Phish. And being familiar with this version can supposedly help us determine which year the MJ comes from. If we're being straightforward, that would suggest the MJ is from 2000. But we're not being straightforward. The post midnight Cypress guess is a neat one but I don't think it's from there.

Maybe there's something about the actual 7/4/00 Jibboo itself that gives a hint about the MJ? Something about the sound? One interesting thing is that the MJ has the boomerang effect in full force that was used in almost every 99 Jibboo. And why would someone point to 2000 in such a roundabout way if the Jibboo itself weren't meaningful?

Or maybe it IS from 2000 and the straightforward comment is a roundabout way of saying it's a Twist jam?

I don't know. But what's that weird horn-like sound half-way through? Seems to me that's the key to figuring it out.