Weakest link?

I wouldn't say any of your current gear is an obvious weak link. The Freya seems like a very respectable design. 

I have LS50s in one of my three systems. Even through they're inexpensive, their midrange and coherency is tough to beat IME. Speakers that have comparable midrange, but greater resolution, scale and rocking ability are Spendor's Classic Series. I have Spendor SP2/3R2s in my main setup.They basically do everything the KEFs do well, but improve on some of the weaknesses. Few speakers can match them for acoustic music IMO, but like any speakers, getting the best out of them requires the right amp.

Other good rock/jazz/acoustic speakers are the Klipsch Heresy IIIs. Surprisingly good for the money and not at all shrill or bright as their predecessors allegedly were. Again, the right amp is required to maximize their sound.

Here's a recent review from a guy who has owned many highly regarded speakers: http://www.stevehuffphoto.com/klipsch-heresy-iii-speaker-review-im-floored-and-here-is-why/

Hmm, a toughie.

I think both the Schiit preamp and the KEF speakers would be candidates for upgrade.
BTW, I love Schiit products. If anything, get one of their DAC's, like a Gungnir or Yggy. Though you could get by with an Ayre Codex, which will do both Preamp and DAC function for a very low cost.
For Speakers, I always recommend Vandersteen. A Vandersteen VLR would be a comparable bookshelf to the KEF.
I also use Zu Omen Bookshelf speakers for my office. Not as good as the Vandie's, they are natural and non fatiguing.
Bob

I just replaced a pair of stand mounted monitors with Heresy III and am loving them.  Sound is big and bold and closest to live I've ever had in my room.   I have had a number of fine standmounted speakers and a sub and the addage there's no replacement for displacement is true.   Little speakers just can't throw a big image like the Klipsch can.