welcome to the club and congrats on getting so many miles out of it, mine went a lot sooner
The general consensus is that its not worth the cost to rebuild. People replace rather than rebuild.
The 6 speed is a direct fit swap for the 5, and 6 speed is apparently a lot more reliable However, the top gear/final drive ratio of the 6 is slightly lower than for the 5, so for the same speed in top gear, the engine RPMs will be a little higher with the 6 than the 5. This will cause a slight drop in MPGs, but the extra cost of gas is way below what you'd pay if you bought another 5 speed and it dies too. I replaced my original with an 04 5 speed, which also died. Now I have an 05's 5 speed in there, hoping it will last. Guess I have a 15 speed Vibe
I would stay away from Ebay for the tranny. Try
http://car-part.com" onclick="window.open(this.href);return false; to find a used tranny near you. Gives you the ability to search all the junkyards near you, or anywhere int eh US, for specific parts. If you go for another 5 speed, then get one that is out of an 05 or newer. Same tranny in Vibes, Matrixes, and Corollas, from 03-08, so don't limit to one that came out of a Vibe. Most junkyards will give you a short warranty, which is good for such a pricey part. Some will even replace it for you.
Lots of clutch options out there, not sure what to recommend