I forgot to mention that, and this could be a stupid question, but the kick sound is noticeably different standing in front of the kick versus playing.
I have news for you:
all your drums sound different from a distance. If you ever have the kit in a venue-sized room, it's a worthy experiment to have someone else play the kit while you listen from 30' away. You'll notice that most of the snare drum ring is gone, tom ring too.
The reso is a stock Ludwig made by Remo. It's labeled as UK drum head. Thoughts on whether this is a tuning issue or a cruddy reso head. BTW, the reso appears to have a muffling ring on the inside and I have know idea how old it is since I bought the kit used.
It could be a real (American-made) Remo PS3 or the version they have made in China as OEM heads. The PS3 is a great head, the Chinese version is okay but not as good. Neither is "cruddy." But they may or may not be what you want or need in a reso head.
I know this is normal to a degree. When playing mine sounds like there's a 12" sub inside of it. From in front it is far more dead sounding. Almost sort of "flappy". I've tried various tunings on the reso and can somewhat even it out. I'm just not achieving the nice "thud" sound I'm looking for. A pillow inside got me close but I lost just about all the volume.
Muffling makes drums softer. That's why they call it muffling.
If you play out miked you can do pretty much anything you want, since your bass drum sound is mostly science fiction dreamed up by the sound guy. But if you play out unmiked, I would stick with the stock reso (or upgrade to a PS3) and ditch the EMAD2, which is a pretty dead-sounding head. Use another PS3 (or Evans EQ4) instead. Tune the reso up a little bit above JAW, up to where it begins to have some bottom end and sustain. Then tune the batter a smidge higher. You will hear the sustain at the kit, but the audience won't--they'll just hear a louder drum.
Bear in mind also that bass drums in particular are very sensitive to their placement in the room, especially smallish practice rooms. Their frequency (ca. 80Hz) is smack dab in the range of the room modes, so moving the drum a few inches here or there can make a surprisingly large difference.