Agreed.
You can get a 90* silicone elbow on the input and run a draw through MAF into the passanger sidefender well easily. Like this..
I have one of these elbows on my turbo and cut the side that mounts to the inlet down to where it's only wide enough for a t-bolt clamp. IMO, there is more than enough room in it's currant setup to pull this off.
SCT's PRP would be ideal for tuning and the usage of a Ford MAF or an SCT MAF along with properly sized injectors for your target power output. Might as well change the fuel pump out if you plan on putting decent power down (Who wouldn't if going to all of this 'trouble'?)
Clock the output to aim downward and run it through a universal type FMIC and run back up the drivers side to the TB. Here is something off of ebay that'd work for a pretty good deal
Low cost FMIC, piping and couplers w/ clamps....... not bad Relocate the coolant resivor and move the battery to the trunk like others have said, and you're on your way to a good upgrade.
As a tuner kit, this would be a good option. I'd s%&^ can the rest of the kit.