If your stock turns to jelly in the fridge, it means you did it right!
Simmering the bones breaks down the collagen and turns it into gelatin; that's the very essence of stock-making. The gelatin is exactly what you want from the stock; at low temperatures it has a very jelly-like consistency, but at higher temperatures it melts and provides a very rich texture.
The more you reduce the stock, the more gelatinous it will become, so if it turned out stiffer than you expected, it's probably because you let a lot of water evaporate. Typically, when making stock, you use a very low simmer; just a few bubbles per minute. Any more than that and your stock will reduce.
But reducing is perfectly OK, and many cooks will reduce an entire pot of stock down to a few tablespoons; it's like bullion, only without all the salt and preservatives. Heavily-reduced stock is called glace de viande and is often used to give a sauce or dish a little bit of extra kick, imparting a powerful meat flavour. But you probably didn't reduce it that much.
If you're finding it to be too concentrated or gelatinous, even at higher temperatures, you can feel free to dilute it. For soups or sauces you can probably dilute it 1 for 1, but taste as you go along just to make sure you're not watering it down too much.
When only the top layer of a stock solidifies in the refrigerator, it is probably fat, which you should skim off and discard (or reserve). The rest is your actual stock, and in your case it sounds delicious.
Also, since you mention vacuum-sealing - I prefer to use covered ice cube trays for freezing stock. That lets you portion it out much more easily than a big solid blob.