The MAS should remain on the intake pipe, The aftermarket intakes should have designed them to stay in. The car won't run without them.
I decided to build my own, and made a pipe extension coming out of the end of the MAS, and places the filter directly above the fender opening. In the Northwest, the water issue keeps me away from a low mounted filter. Yeah, I know, there's the AEM bypass, but this way I'm sure it's safe.
I didn't worry about the temp. sensor, just put it next to the filter so the computer knows the temp of air at the filter, just like the stock box. I also read that the computer doesn't even really do much with the temp. anyway.