Just wanted to add one last post to this thread to serve as my conclusion. After less than 100 miles were put on the transmission, I started noticing a weird sound right before/during shift transitions which reminded me of a 'bullet ricochet' sound. I know that sounds pretty generic, but that is the best way to describe it. It sounded like extreme pressure being amplified by passing through a small orfice every time the transmission would shift through any gear, with the 1-2 shift being the loudest. I talked to Chris and he didn't think this was anything to worry about although once again this is a sound that I have never heard a transmission make before(?). I continued to drive the car for a couple more weeks, and about another 400-500 miles and the sound slowly became less apparent. During those 400-500 miles I finally made it to the drag strip, which was a goal that I started to wonder would ever be possible with all the mishaps this driving season presented. I got to run 4 times that day, and after my first pass I was stopped by the track official on my way back to the pits who informed me that the official at the start line noticed a few drops of transmission fluid on the track. He told me to see what I could do about fixing it or I wouldn't be allowed to run again. I jacked the car up, and once again (just like the first transmission) I noticed the servo was leaking fluid. Also, the shift lever/shaft appeard to also be leaking. I cleaned everything up as good as I could and got to run 3 more times without anyone noticing fluid leaking. I ran a best time of 13.30 @ 103.36 MPH on my street tires that I drove to the track on. The transmission was shifting into 3rd too early at about 5000 RPMs which is about 500 RPMs lower than the 1-2 shift. I believe I could have manually shifted the car and got a slightly better ET by allowing the motor to rev a little higher before the 2-3 shift, but I was winning rounds in the trophy class so I didn't want to change anything from my previous runs to stay consistant. I did end up winning the trophy class that night which was a great feeling considering all the heartache that I had to endure this year because of my transmission issues. That was on Saturday, 8/24/2013. Two days later on my way to work at 6:50 AM an 84 year old man pulled directly out in front of me at an intersection which resulted in my car being totaled

Unfortunately, I will never get the chance to see if this transmission would have lasted during the warranty period which will expire in Feburary of 2014.
After a month went by since the last transmission was shipped, I was contacted by CK Performance asking if the container that the transmission was shipped in could be returned although at no point in time during several phone conversations did anyone from CK Performance ever mention that they would need the container back (an old Ford AOD black plastic crate/container), so after a couple weeks of it sitting on my porch I threw it in the dumpster at work. Also, I was asked to provide the pictures I took of the 2nd transmission that arrived damaged. This is something I already provided via email almost 2 months earlier, but I'm not really surprised considering I have never managed to get CK Performance to respond to any email I have sent in the past.
At some point after I decide what route I will take in obtaining another vehicle to put my motor out of my 86 MCSS in, I will then try to have someone in my area go through the transmission I got from CK Performance and determine if it is worthy of installing in another vehicle or wheter it would be best to just try and salvage whatever performance oriented parts (like the billet forward drum I believe should be installed, the CK Performance valvebody, and CK Performance servo, etc) and have them used in the present 2004R after having all the leaks corrected and clutches examined for any premature wear/etc or just to go with my initial plan of installing a manual transmission which will probably prove to cause alot less headaches in the future.