Is there any difference between this and the naga jolokia sauce?

Yes there is. There are different varieties of Ghost chiles, and this sauce doesn't specify which it's using. The flavor is more chile-fruity (in the way a Scorpion pepper is) than Melinda's Naga sauce (Naga is a specific type of ghost pepper) which has a "dryer" heat and a -slight- bitterness. HEAT: They have about the same amount of heat which is very hot for an experienced hot saucer, but not nuclear. Beginner saucers will find these too hot to enjoy and Chile-heads would describe these as "medium". Which is better? They're both better :D -- it's not redundant to have both of these sauces in your cabinet: a fun palate experience is to try one after the other on the same food and discerning the difference.

The million scoville mention on the bottle is about the Ghost paper, but what's the scoville rating of this sauce?

You should purchase the vastly less expansive El Yucateco Chile Habanero sauce. If you use 3 times as much it will save you money. Depending on the Hispanic pop % of your residence, you can probably find it -- even at WalMart. (I can and I live in NW Ark which has relatively few Mexican Americans.) Experiment.