I have had very good luck using three open source, free programs: autopan-gui, hugin, and enblend.
I'll be the first to admit that they are not user-intuitive, but there are GREAT tutorials that take you through how to use them step-by-step. Now that I know how to use them, I find the process very quick. Hugin is great because you have the option to export into PSD with mutlilayers. You can have it pre-make the masks or you can just have it align and rotate the images and you can blend them yourself. I generally export to multiple tiff files and let enblend do the masking and color adjustment. I find that 90% of the time I cannot tell that it was was a multi-stich image even when viewed at 100%. The times where there are errors, I re-stich the image into Photoshop and get to work.
Just wanted to share the results from the free, "no-frills", student-friendly solution. I think the programs work great together. If anyone wants to know specific tutorials or if you have questions just let me know.