Okay, definitely run the dual factor version here then:
http://www.elitefitness.com/forum/showpost.php?p=4764723&postcount=381
If you want to clean you can substitute them for rows on M/F and follow the exact rep scheme. That's an option.
You can also substitute cleans or high pulls or clean pulls for the dead on Wednesday, that's another option. You can also combo this with the above in some way so that you are doing cleans M/F and clean pulls on W.
The main issue with doing Clean and Press on Wednesday (just fogetting about any cleaning on M/F for the sake of argument) is that the clean is going to take away from your presses. You will press more without having to clean the weight each rep. If you are worried about upper body strength this is going to affect your overhead work. In addition, it's just too much pulling volume after deads. Your body is going to be wrecked. Squats, deads, and clean & press in a single workout is going to be very taxing. Maybe with AM/PM sessions you could manage a bit better - maybe split it into 2 days. I don't know what to tell you other than many people with decent lifts dread the Wednesday workout in the loading phase and are at their limit in weeks 3/4. Very few people can tolerate this extra work and I don't know anyone that can set records in the 5x5 dead and the 5x5 clean and press after squatting 5x5 in a single session without almost dropping - unless of course their press sucks so it winds up being not very taxing. The other side of that is you can start it and see how it goes for you. It's easy to drop and just press from the rack.