Getting that out of the way I do have some suggestions for your system. Most of them will be around $1k, but you don't have to do all(or any) of them.
I will start with your turntable. Yes there are better tables out there, but do you want to spend at least $3k to $5k (for starters) to really hear what vinyl had to offer? There will always be a better turntable than the one you have. You have a decent turntable and a good cartridge. The Ortofon 2m Bronze shares the same pickup as the 2m Black. You could try the Black stylus out...it would be a quick and easy swap.
You could also upgrade to a SoundSmith Carmen. It would give you a different "flavor". The other upgrade would be the Decware ZP3 phono preamp. There are a bunch of upgrade options when you order and I definitely recommend getting the capacitor bypass mod. It will give better performance during transients. There are also many other great phono preamps out there and to beat your Schiit Mani you need to spend five to ten times as much as the Mani.
Now let's talk some Schiit about your DAC. I have the Gungnir Multibit so I have to say good choice on the Yggdrasil. The best advice I have gotten on preventing upgrade-itis and boredom is to have two of something like DACs, turntables or speakers that can be easily switched. So maybe get a second DAC that is different and have both of them hooked up and ready to go. Have your CD transport hooked up to one via Toslink and the other by coaxial. In a couple of months I would swap connections to see if one DAC does Toslink better than the other.
I don't have anything to say about your amp and preamp choice because I have not heard them for myself. I just spent the weekend auditioning three different Decware amps and the CSP3-25th Anniversary preamp. You like what you have and there is nothing wrong with that.
Between your preamp and your power amp you have a Lokius...at least that is where I would put it. Decware has a Zrock2 tube Equalizer. It would be something to check out. Before Decfest my next major purchase was going to be a ZP3 phono preamp...now you can add a Zrock2.
I do have a speaker suggestion. I will also stress that it is in addition to and NOT a replacement for your current speakers. This goes back to having two very different things for varaity. Check out Caintuck Audio's Betsy Open baffles. I spent a few hours listening to Steve Deckert's personal pair of the Betsy Alnico speakers. He was gracious enough to dig them out for me. They have an eight inch full range driver with an AlnicoV magnet.
At home I have a Betsy clone I made with a Lii Audio F12 (12") driver to compliment my Decware Imperial speakers. These open baffles are easy to move around so they can be tucked out of the way when not in use. Placement is not overly critical, but they do like to be pulled out at least three to four feet from the walls. The imaging is insane and the simple beauty of a single full range driver is haunting. I am recommending an eight inch driver because you already have subs.
I had a lot of fun putting this together. I hope it helps you.