The 2 main metal clips are to the roll bar. You'll want to start prying from the outboard edge where the window was. Then there are two plastic hooks holding this panel onto the lateral trim piece. Also note that this panel is sandwiched underneath the forward trim (where it says AIRBAG), you'd...
Unfortunately this is true. You would have to step up to Badlands to get a manual and Mid Package.
To sum up, Manual is only available on 2.3L for Base, Big Bend 3/5 Standard, Black Diamond 3/5 Standard, and Badlands 3/5 All Trims.
Looks like you can fit two MTBs in the 5-door similar to baby Bronco, but you'll have to remove front wheel and lower/remove the seat (to clear the cross-beam). Not sure if there's a fork-lock in the works, but you could bungie/ratchet-strap to the tie-downs.