The boost valve needs to be installed as shown in the picture below. The left-most part is the pressure control valve which "usually" does not come out when you change the boost valve, but if it does, stick it back up with vaseline.
I don't understand your Q about "clocked a certain way". It needs to be installed as in my pic. If unsure, PM me and we can set up a time to talk by phone.
I would personally never use RTV within the trans, but I know an expert suggested this to you; just be careful.
While it is best for the PCM to know when the trans is in reverse, this is not necessary for Reverse to work. Even if you remove the trans connector, reverse will still work.