A call to Patrick's yesterday solved most all of the problems. I spoke to their head mechanic who helped me out with the process. They are also putting the correct shifter in the mail (UPS) for me and shipping it 2nd Day since it was their mistake.
When choosing a transmission the only thing I looked at other than the ratio (look for the two grooves on the input shaft) was the condition of the gears themselves. I pulled off the side cover and looked inside. The synchros and gears all looked good with no visible chips. I pulled mine off a Vega (not sure what year).
As a side note, has anyone who tackled this swap also attempted to put in a dual cylinder master cylinder? I am finding that there are some clearance issues. If anyone has a remedy I am all ears. Thanks.