Got a performance built 2004R from a very reputable shop that deals with those transmissions, but I installed it incorrectly. I'm tearing it apart now to try and figure out if I hurt anything and I'm seeing some differences from what the Haynes manual says. Can anyone verify these changes were made to increase performance?
1. I've only found 7 check ***** and the manual calls for 11.
2. There's no oil deflector plate behind the oil pump, the manual says there should be one.
I'm not done tearing it down so there will be more questions to come, as always any and all help is appreciated.

 

Have you attempted to contact the "reputable shop" that built the trans for you? They might not be happy to find out you are tearing into the valve-body (possible warranty issues), but they should at least be able to tell you the answers to your questions.

How was this trans "installed incorrectly", and what makes you concerned that you caused harm to it? About the only reason you'd need to pull the pan for an initial install is for the TV cable setup, and about the only way to cause harm is to not have enough fluid in it and not having the TV cable setup and adjusted properly. Did you use a pressure gauge to verify proper pressure response when the TV cable (throttle) is blipped?