I'd be supprised if you can stitch that many together in 1 image sequence. Of course if your thinking of something just thumbnail hight you should be ok.
However if you wish for anything say for example 400 pixels high or above.
The file size will be gargantuan. I wouldnt be supprised if your image editing app throws a wobbler mid way. - you'l need a lot of ram.
From my experience flash does not like large images scrolling from off screen. It turns into a juddery mess even on the highest of spec systems, and you will probabbly hit image width restrictions after maybe 5/6 stiched images. so you will have to create 50 odd satggerd layers of say 5 stiched images triggering off the previous. - all a bit of a fiddly mess. It will still most likely be jerky on playback. and will no doubt not join the seams properly between the transition of layers.
My advise would be to align them using the tools suggested above. or try
http://www.ptgui.com/ - You will still probably have todo it all in multiple sections as there is no other obivous way I can see to get around the huge width the final image shall be.
Once the images are aligned, I'd take them into a video editing /composting package and create 1 video of the whole scene scrolling at your preferable smooth rate.
This video file can then easily be made to stream via flash, with a little extra work add a feature so it can be scrubbed/scrolled back and forth at will.
The resulting quality will be a lot higher. Panning images do require a nice smooth playback or they look a it rubbish.
