The stock box is too restrictive at the higher R's and WOT.
Most ANY free flowing intake will be better - enough so you can feel it. To feel it the increase has to be almost 5%.
You can use the original duct, cut it off, and fit a K&N on it.
You can buy a metal one - short or long.
The "cold air" - the difference is negligible. Sure high HP race cars do it, but not through a long duct like that. Look at the way do it, entirely different! Even then, at 900 HP it could add an extra 2 or 3, HP, it's not felt, but it can make the difference in winning. If you need to increase your ET by .0003 sec, consider it.
There are lots of "dyno proven" High Performance things out there - the "high performance" is their profits, not your Jeep.
For the squeal on that one, try positioning it slightly different. If it's just when cold, it's your IAC.