There are two different extensions needed for the 2JR intake.
First is an extension for the wiring harness for the MAF, they're like $50 on Amazon (line somewhere in this thread) or alternatively you can cut and splice your own in for the cost of wires/connectors/etc. This harness will extend the stock connector (connects right after the intake lid on the stock system, the only electrical connection on the intake I think) to the new location across the engine bay.
The second is the MA Performance intake adapter that's required for all 16+ FiSTs. You would also have to lengthen that with some vacuum tubing I assume.
Keep in mind, I am stock and have not dealt with any of this first hand, just going off of what others have told me on here and what I've gathered doing research on this intake. Hopefully I'm not too far off...
The Cobb wins for me over the CPE in function, but the CPE is a much more aesthetically pleasing intake. The thermoplastic construction of Cobb is what wins for me...if only it came in red. I think the Cobb will perform best due to the plastic being more resistant to heat soak.