i always used ps cs3, it does a good job, i always found it stiched raw files better than jpegs for some reason
The biggest problem here is you've not over lapped the images. When shooting panoramics you need to over lap each shot by at least 25%
The more you over lap the better.
Any stitcher is going to have a hard time with these as they are basically butting up straight next to each other.
You've done the right thing in shooting portrait thought this will give you more flexibility once the image is stitched.