Intake and Possible Shifting Problems?

Alright I have a few questions:

1) I just installed my intake and had to remount the PCM since it was originally in the stock air filter box. Right now (see 2nd picture) I have the PCM sitting zip-tied down and covered with some temporary bubble wrap to keep it from getting wet if it rains. I don't think it's a good idea to get the PCM wet, right? Since I built the intake with a friend of mine (besides the K&N filter), I need to figure out a way to keep the PCM in place and dry. Any ideas on how I can do this, or anyone know someone who can make me a case to surround the filter/PCM like the picture below?


Here's a picture of the K&N set-up in a monte carlo. Note the green highlighted area being what I was talking about to keep the PCM in place and dry and where the PCM is.


(Bottom right is where my CPU is sitting zip-tied and wrapped up in bubble wrap to prevent getting wet)


2) My car has recently been having trouble starting, it wouldn't start one day leaving school, so I had it towed to the dealership. They found that it was a bad mass airflow sensor (MAFS), so I got that replaced. Meanwhile, now that it starts fine and such, my car is still sketchy shifting. After the car shifts to a different gear, the RPMs will go up and down a little, shaking the car a little, but then drive fine. Not too sure what this is, and maybe this may be causing the check engine light? Anybody have any ideas? I can put a video of it on youtube if that will help you understand what I am talking about. My tranny fluid/filter is good.