I am a little late for chiming in but better late then never.!!
Josh, I first put a flow 50 dual in dual out and definetly noticed a low end loss and mid range boost (a little anyway on boost). Also I was getting a lot of resonance (not drone), the kind that sounds like valves slapping. But I also had opened up to 2.5 from cats back (no resonators) so I was flowing more free then you are. Dale and I talked and decided to try a magnaflow 5x11. Magnaflows are a bit quieter but still very aggressive sound and have a built in crossover. A good bit of low end came back but not all. I can't tell you whether this was from the crossover or magnaflow having more backpressure. I am convinced the low end loss was due to backpressure loss. A certain amount of backpressure is needed to keep that low end alive. If you can get a reasonable price quote on a H pipe installed it may be worth a try but as Dale said, maybe wont help. Opening up the pipes to 2.5 really boosted the mid range throttle but the price was low end. As Dale and I were about to experiment with some dynomax super turbos, I ended up with this new truck so back to scratch for me. Dale are you going to try the dynomax?
It would be nice to figure out a way to be abke to control back pressure with a adjustable baffle to experiment, that would answer a lot.
After I typed all this, I realized I really havent given you a solution Josh, mainly because I didnt come up with any before trading my truck in. I do know the magnaflow improved over flow 50 for my setup which was similar to yours except the additonal opened pipe I had. They arent real expensive. My muff guy put the maganflow on for 100 installed. I do believe single in 3" is way to go instead of dual in dual out. I was thinking my next move after dynomax would have been single 3 dual 2.5 out magnalfow. But I also was dealing with sound, trying to quiet it down some. You can also look into resonators (bullets) in front of your flow. This is going to quiet it down a "little" but should create some backpressure as well. Muff guy here was going to put some on for 30 bucks installed for each. Actually that may be best route for you. It is a 60 dollar gamble but may work. If you like the sound now, it will probably be same just toned down a bit as far as decibels. It may get rid of some drone if you have that as well.
I think it is worht a shot. Call around though, one shop here wanted 70 bucks for each and next was 30. :?