My local guitar shop has a New Old Stock Gold Top esp ltd ec-400at. My question is will i be happy with this guitar or should i save up a few more $$$ and buy a new 2011 ec-1000 gold top? Also what should i expect to pay for the ec-400at?
It's similar to the 401VF's, but it's older, and the AT stands for archtop. I would say it's pretty close to the same as the EC1000MGO, except I believe the 400AT has a more "vintage" neck profile, and it's considerably thicker.

I wouldn't pay more than $400-$500 for it, considering a new 401 is $630.
I highly doubt the neck profile is any different on an LTD, but it's possible. Eclipses really aren't my forte when it comes to ESP.

The body may be thicker. I know some of the EC's have what they call a "full thickness" body, to try to replicate that vintage Les Paul tone better.

In any case, anything 400 is bound to be better than anything 401. LTD's quality has decreased over time, and generally the older model you can get the better.
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Theres 2 on ebay right now buy it now at $770... ouch. How much were they back in the day new?
I'm pretty sure the neck is a little thicker, I've seen them in photos, and the neck profile definitely appears to be a little more chunky than the standard neck profile.

Back in the day new, the MSRP was $849, I'm guessing the actual price was about 30% less, so they probably sold around $600. The only reasons why they would be $770 is because they come with a case, they're more sought after because of the quality and/or the gold top was a limited color.