Hi!

! Good for you for taking those three goldfish! they do sound like they need some help - FAST! A cooler just isn't going to cut it for three 5 inch comets! but, you already know that because you came here!
First off, the 44 would be fantastic for them! But, if you do not have it available right away, another great, not too expensive, and easy re-useable solution is to get a big rubbermaid tub form the hardware store! Since you mentioned that you could do an indoor pond - here is a link to a pond I have that would suit the need and is also reasonably priced and easily converted to another use later:
http://www.petsolutions.com/popUPpond-I-30790028-I-.aspxI can't even use the one I have - I'll send it to you! I would recommend the 45g.
If you use a tub or a rubbermaid then you can bolster the sides with bungee cords form any hardware store.
The main thing would be to get the fish outta the small cooler as soon as posible. If you cannot afford a 400gph filter right away, then I would suggest that the bigger the "tank" you can get them in, the better! More water means more dilute toxins - you will just have to change it 50% everyday until you get a filter.
It looks like either way you are going to have to cycle. The water they are in right now is not cycled - it is just plain bad. I would slowly add water the container they are in until you can tranfer them to a larger coontainer of similar clean temperature and pH matched water. Adding a bit of salt won;t hurt either - at the rate of 1 teaspon per gallon of water.
I would not bother with the UGF. it won't do much of anything until it is cycled so it won't make much of a difference now. I would concentrate - as you put it perfectly - on clean water right now! Water changes and some TLC are what these guys need!
Sinking pellets are better food for goldfish - you are right again, surface feeding can cause air to get trapped inthe swim bladder causing flipping. But, so can high Nitrates! A harder condition to reverse. So, I would get them asap into a bigger container of fresh water, feed sinking pellets, and definitly add an air stone.
Warming the water slowly would be nice for them although tey are dclearly used to the low temp - however, it is hard to tell their reaction because they do not have enough room to show you if they are moving around or not! I mean, if the container is small, then they are sitting on the bottom with clamped fins because they have to! So, ideally about 72-77 is great for GF - but as long as it is done gradually, it is safe - the problem is a sudden and dramatic change (>2 degrees, for example).
I am trying to answer all your questions but I have to admit I got a little confused about what the exact plan is now... I would really like to help you get them settled - because it was so nice of you to try to help them!
PS - I can spell but I am a terrible typist -please excuse. I try to correct but I don't catch everything.