I have recently started to play with Panography, which is a style of stitching pictures together, however on my first couple of attempts, quite a few of the pictures that I took were distorted towards the middle of my scene; many of the objects weren't correctly aligned. Is there any way to remove any way to remove this distortion that before I take the picture?
It's hard to give a specific answer without knowing more about your post process workflow, but here are a few things you can try:
However, I think your best bet is to try better software. Photoshop has a panoramic feature that handles distortion, color differences, and other abnormalities quite well. If you already have Photoshop, it's under File -> Automate -> Photomerge. There are other software packages that may also do a good or better job.