When looking to do this swap, I only found two sources for step by step procedures on swapping the 3.4 into a boxster. Both had the flapper valve towards the front and top. I just assumed that's how it had to be. Going that direction does not leave you much room at all and that's why I decided to notch the area around it. I really have to thank cbadbox for the pic. I tried it like yours, and there's soo much more room flipping it over like yours. I didn't need to notch that area but I'm glad I notched the area by the intake runner and intake horn. I like having the extra space if need be. My Chinese headers hit the aluminum brace a little, so I'll notch that a little too.
Another bad idea was trying to bring the shifter cables under the intake. I thought I read somewhere that was better than going over everything. It's not! I had to take everything apart and bring them back over the intake. Another great tip. Make sure you connect all your electrical connectors correctly and securely. I had the cam position sensor and the crank position sensor switched. I also didn't have 4 & 6 injectors fully connected.
It's alive!!!!!
https://www.youtube.com/watch?v=8OiUb9IOMj4
My oil pressure gauge works but I had it disconnected at the time I was taping. My water temp does not work though and I'm betting that's because the 996 I pulled the motor and DME had the 4 post temp gauge and my 3.2 engine wiring harness used the 2 post water temp gauge sender.
I'm using the factory trans mounts because the one's I had were good and I was too cheap to buy new mounts.