Okay, I'm not going to get into "which is better" when it comes to the JLT or FIPK. They are very close to each other performance wise.
You do know that "Tucker" is a.k.a. "Jay", right? I think JLT is Jay Tuckers initials actually! I may be wrong on that though.
You metion an under-hood model or a firewall model. It's not really "firewall", it's "fender". JLT makes 2 different CAI's for the 03/04 Cobra. One is a CAI and the other is an RAI. The RAI is comparable to the K&N FIPK as far as both are being open element/under hood style intakes.
The JLT CAI is an "in-fender" unit and really cleans up the appearence of the engine bay by relocating the MAF & filter into the fender where they can't be seen. Keep in mind though this makes servicing the filter a pain in the butt! Plus I don't think there is a measurable difference between the CAI and RAI as far as HP & TQ are concerned.
As for the K&N being a Gen I or a Gen II... I don't think you'd be able to find a Gen I if you looked. They are not being made any longer so any FIPK you order will be a Gen II.
U.M.