When I adjust the image size in photoshop (I know thats not the actual fact of whats happening) it also changes the size of the file itself. If I do all my scaling in photoshop, write down what print size equates to the scale I need, and save the original un-enlarged version, this results in a smaller file size. It seems like I can then take that smaller sized file and use QI to handle my enlarging. This seems like it would avoid the issues I was causing myself earlier. Is this an accurate understanding?
I'm not sure if I follow the workflow you describe, but it sounds like you are going to have multiple interpolations.
After the stitching process, you do end up with a file? Right?
I don't know the file size, but if you can open that in Qimage, then set your print size, like 40" x 72", and let Qimage Ultimate interpolate one time to get the 360 ppi native input for the 9900.
If you want to sharpen or make lighter, darker, more/less contrast/saturation, etc you can do all that before printing which is saved as a filter in Qimage.
... and yes, 200 ppi is plenty for your prints.
Fred