Trouble In A Hurry

So I rescaped my 20 gallon this weekend. Now I'm having issues..and it's only been two days. Because I'm so bad at describing these things I figure I'll use pictures to say it for me. This is the same tank I wrote about concerning the shrimp in the Invert Section. Am I underdosing (though I don't see how)? Lack of CO2 (even as it appears I may have gassed my shrimp)? The light sits about 10 inches above the tank so that shouldn't be an issue. The bottoms of stems are turning brown beneath the substrate, leaves in general are dying, crypt has holes now and L. arcuata looks as though the color is "peeling" off. It's only been 48 hours!

 

Actually, yesterday the water smelled kind of like..fresh asphalt? I did a 50% water change and today it smells better, but if I rub my fingers together beneath the water's surface it still feels a bit greasy.. More so than tap water anyway, but maybe that's normal. I'll do another water change today, all I have left is my otto and I'd like to keep him alive.

One shrimp died overnight, but one made it into the morning. It was at the back of the tank on its feet but wasn't moving around much. When I got home he was dead in about the same spot he was lying in yesterday. These shrimp were literally an inch apart from one another when they all died. If the suspected culprit is ammonia, then I'm a little lost. The tank sat as a "mini-DSM" for about a week. Then everything was fine after I added the livestock and plants. The substrate was about 2 1/4" deep but it didn't look too good to me, so I added more sand this past weekend and it totals 3 1/2" at it's deepest point. What happened to the bacteria that would have been in the substrate and in the filter?
As a positive the L. arcuata and M. aquaticum both are producing side shoots that look decent..but the main plants are absolutely fried. The glosso is standing up so it seems to be responding well to something. The crypts are hurting like crazy, it took me a year to accidentally get my swords looking like my crypts do right now.
If I was to aerate the substrate (poke down to the worm casting layer with a skewer) would it help the substrate right itself, or help anything in the long run? I can't do it on the glosso side too much but the stem side is fair game.