I swapped out the transmission myself with a used transmission I bought for $300. Everything seemed to go pretty smoothly. Then after I put everything back together and started it up I put it in reverse and I got a whining sound and the transmission wouldn't engage. There was a loud clunk when I put it back in Park. The transmission did engage when I put it in drive, and S3/S4 but not in 2. I took it on a test drive and the tranny would not shift automatically, and when I manually shifted it only went into 1 & 2 gears. I noticed that the S gear light on the dashboard was flashing and the LED light under the floor board on the passenger side was flashing 17 times then pause and repeat. My manual doesn't go up to 17 flashes so I'm not sure where to go next. I believe that it may be something electrical or and control cable. What about the seleniod connectors, if I connected them backwards would this happen? I was hopeing to see if anyone out here has any thoughts or suggestions. I was told that the tranny was working fine when it was removed it from the previous car. Is there anything that needs configured when swapping a tranny? Does anything need to be lined up a specific way? Thanks in advance for any help or suggestions.

-Dave