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If the still are numbered in sequence, then check the Help file for the Numbered Stills options. That should get you want you need.
I did not realize I had to check the "numbered stills" checkbox when importing my frames, and did not know this was called "numbered still-image" (to find it in the help)
You mentioned 'several thousand' files. I can tell you from personal experience that Premiere is more than likely going to hang up after a certain point with those still images. I did a timelapse movie with over 70,000 stills, and I couldn't get Premiere to handle it. The answer to my problems was After Effects. Hopefully, you have the suite that includes AE. If so...
Open After Effects. If your stills are all in sequential number, like DSC_0001, DSC_0002 and so on, you're in luck. Click 'import' and choose the first image (0001) and note that the sequence checkbox is checked. Get ready for magic, because when you click 'open'... *poof*... you'll see a nice stream of all the images arranged in order for you, one frame each. The beauty of this is that it maintains your image size. Say you're shooting 16 megapixel images. You'll have this massive screen size to work with, and you can "down-res" the video to HD or whatever you're using, and pan/zoom around the image very easily.
Pretty neat, huh? Export to the size you need, and you're done!