I would suggest trying Photoshop again. Sounds like you are doing it manually which is painful. Go to the file menu then to automate and select photomerge.
You will be amazed! Select the type of effect you want, I use the reposition one, browse for the photos you want to stitch together, arrange them in the right order, click ok and your done.
It awesome!
MikeM
Pixel This Photography, Inc.