Okay, I've spent the last week or so test riding bikes and have rode Fuji, Felt, Trek, Lemond, Giant, Cannondale, and Specialized (eh, I may be missing a few here). Anyways, I've gotten two entirely different opinions on fitting, even for the same exact bike!!! For a little background, I'm 5'2", have very long femurs according to a couple of the LBS guys, relatively short torso, and have been riding MTB, so sitting fairly upright.

One group thinks I should be on a 43-45cm bike, mainly because when I climb on it I feel comfortable immediately, no actual fitting or alterations other than looking at stand over height and adjusting the saddle height.

The other group thinks I need a 47-48cm. This includes the guys who have helped me extensively with my MTB, and they were the only ones to do any type of actual fitting, and one of the other shops. When I climb on without any changes being made to the bike, I feel stretched out, but to these 3 guys I look like I'm in the right position. After doing some changes to the bike, including moving the seat backwards based on what my knee needs (opposite of what I feel like I need to be comfortable, but after researching a little bit and looking at how I fit on the other bikes, my knee was way too far in front of my feet) and changing the length of the stem, the number of spacers, and the angle of the stem, and ajusting the brakes, this size felt just as comfortable as the smaller bike. They also took the time to explain to me what angles they were looking at and what to look for when I test ride the other sizes to see if the bike is the right size. They also altered how I was sitting to a more correct position, which also made me more comfortable.
The way they explained this to me was that I am used to sitting upright on my MTB, which with the smaller bikes, especially if the seat wasn't moved back, I would fimmediately feel more comfortable on because I was so much more upright. They felt that the smaller bike would work for me immediately, but that as I got used to being more stretched out, the length of the stem would have to be lengthened to the point where I would be too far out front and wouldn't have adequate control over the bike.
I really did feel comfortable on the larger bikes after they made the changes, and didn't feel like they were pushing me towards the bigger size just to make the sell as they had the smaller bikes there and were switching me back and forth between them to see which one did fit me better. For reference, the one store had me on the Specialized Dolce and Dolce elite, and the TCR 1. The other store of this mindset had me on the Trek 1500 (but they only had the 47, so nothing to compare to at that store)

Which way sounds right to you gals? I'm wanting to make sure I get something that really fits me for the long run as I want this bike to last. (also I might add aero bars over the winter as I am using the bike to do triathlons)

Sorry this is so long, and I hope it makes sense.