A couple of thoughts;
A) As has been pointed out many times, that's a L-O-N-G path for the air to travel;
B) every tight bend in that path creates friction on the airflow;
C) That flex pipe (and there's a LOT of it) has 2 issues;
1) because it IS flex pipe, it'll flex inward as vacuum is drawn by the engine intake; &
2) due to it's shape (plus the shape it assumes under vacuum) all those ribs (and spaces between) create disruption to smooth airflow;
D) In addition to the (old) cap-type being in a low-pressure zone, its shape may receive air-force from the forward side (not that much, since it's a semi-solid wall, it'll actually build a wall of air in front of the filter), but it's creating vacuum on the rear side (higher % than force on the front side) - the faster you go, the greater the vacuum.
Something you might want to consider about the new ram-air intake; put some ribbons (like the tassels on a little girl's bike handles) around (as in, "in the area of" ... like, on extensions) the intake, and, as you drive - check out how they blow around. This will give you a visual indication of how effective the the scoop actually is at "air-ramming". You might end up undercutting the scoop to increase airflow into it (or something).
As for the suggestion about placing the intake in the high-pressure area at the windshield base ... I guess, if it works for you, then it works for you; but I don't know why someone would go to the trouble (+ cost + cut up the hood) to raise the air intake only 3-5 inches.
Just my $0.02
NOT to hijack the thread, but ....
BTW - anyone know a good seal for the MC2100/2150 from the snorkel piping? Will the intake head from a later 4.0 (fuel injected) work? Will the TJ intake cap (as shown in the OP's photos) fit and seal?