Replace C28 with... ?

Do you have plans on your future DAC? If you are just using the HiFiBerry as DAC, it may be extremely challenging to plan the proper preamp. In my experience, a preamp is just another tool in shaping the sound from the source.

You went towards a Bryston preamp. This is definitely on solid state side (no Class A, no tube). You are going to want to put some sort of tube or Class A device in your originating equipment. Your HiFi Berry is probably going to put out very weak sound - there is really no power supply capability in this - I think everything runs off USB power or similar. There is no beefy power supply to push bass/midbass weight or punch. I would suspect the sound is very thin. A powerful preamp may help translate more bass, but it will not change the source waveforms much. The type of DAC may influence the type of preamp you’re after. For the HiFi berry or a different solid-state type DAC, I might look at the BAT preamps because of bass translation (BAT is very good at bass). If you are getting a tube DAC, I would lean towards a very solid state preamp - like a Krell or even a Wyred 4 Sound STP-SE (which is almost like a passive preamp with gain voltage).

Most of your suggested preamps are seriously old school. The Krell is from 1992. Most of this stuff will have to be re-capped (electrolytic caps) for them to perform well. From the list, I would probably pick the Conrad Johnson just because of age. Though, if you tried to find a Krell KRC-3 or KRC-HR and then re-cap, that might be extremely nice.

When I say "old school", I really don’t mean anything negative about it. The circuits are all good. What I’m really saying is that you’ll want to replace all the electrolytic capacitors - they do dry out. The Krell KSL is from 1992!!

Suggestions would be based on what you feel you are missing. Do you feel like you are missing bass punch/weight and low midbass body? Or maybe bass is okay, but you’re missing resolution.

If I had the HiFiBerry, I think my first thought would be to go after the BAT VK3i there’s one for $899. That would give me the bass/body.  The BAT stuff has extremely good bass, but some find it lackluster in the high frequency detail and excitement. You could always start experimenting with tube choices. New tubes are still being made and the industry is not going anywhere.

Otherwise, there’s a Krell KAV-250p for $725. This will probably give you more resolution, but you’ll want to replace all the electrolytic caps.  Maybe look into Conrad Johnson to see what the general sound signature is like (I don't know anything about it)

The McIntosh stuff is generally very laid back and may feel like you are missing resolution. Since you like where the Bryston took you (with more articulate instruments, etc.), you may want to lean towards Krell (or that Conrad Johnson).

What’s your budget for preamp?

It's probably a wash between these two.  KSP-7B is from 1990.  KRC-3 is from 1995/96.  The both would need to be re-capped. 

KSP has an external power supply that is easier to recap, and has a phono preamp. 

KRC-3 may have slightly better input stage, not sure.  I would probably lean toward KRC-3. 

You'll have to let us know how the KRC-3 sounds. 

I agree with mhztweaker on the caps.  I have spent the last several years modifying audio circuits and have gone through a great selection of capacitors.  The Nichicon Muse KZ are the absolute best, in my opinion.  They are extremely fast and very neutral (and provide very detailed sound).  Otherwise, if the KZ do not come in the proper rating or physical size, choose other Nichicon caps (like KW or ES, etc.).  Do not use any of the 105 degree and above caps.  The 85 degree actually sound the best.  I had several people at DIYAudio tell me to use 105 degree caps.  However, they really sounded bad - had some bigtime electrical resonance happening.  The 85 degree caps, and especially the Muse KG, are built to reduce electrical resonance as much as possible.  This is extremely important in audio circuits.  The 105 degree (and up) caps are built to operate in a higher temp situation (like in a car or industrial machines) and do not focus on electrical resonance.

I did not like the Nichicon Fine Gold FG series - they pushed the upper midrange too much for me.

The re-capping with Muse and other Nichicon will make a significant difference in your preamp.  Don't be afraid to increase the capacitance of the two main power supply caps (if you can).  However, the smaller pre-regulator caps should not be larger than about 330uf.  The small caps around the audio circuits themselves should not be larger than 47-68uf.  Putting large caps here will make the sound more laid back with less midrange.  Even 100uf is too large and too slow to respond to the upper midrange transients (you'll even lose some midbass because it's just not fast enough).

Not sure why the Krell manual states that both should not be used at the same time.  It looks like the traces on the board just connect the two outputs together (like a Y-splitter cable) as shown in the upper left part of the following picture:  

http://img.usaudiomart.com/uploads/large/1027567-krell-krc3-vintage-preamp-at-its-best-legendary-krell-sound.jpg

It may be an issue with driving two different types of amplifier impedances, not sure. The other alternative would be to use a Y-splitter cable, which is doing the same thing and you have multiple cable connectors that are degrading the audio quality.  I say that you should just try connecting both XLR and RCA outputs and see how it goes.

I suppose you could use the RCA input/out of the Polk subwoofer to connect on to the Bryston amp, but you'll definitely be losing sound quality here.

If you have any interest, I would be willing to do the re-cap job for the cost of the components plus shipping plus $100-150 labor (depending on what you wanted done).  It's probably a couple hours of work for me.  If you don't have a good desoldering gun, it can be extremely difficult to remove solder and dis-attach the capacitors.  It is easy to pull up traces on the circuit board if you are not able to melt the solder enough - and you've just destroyed a $1000 item. lol. Sometimes you have to re-apply new solder and re-melt the contacts to get all the solder hot enough so that it lets go of the capacitor leads. 

Oh, expect to have a burn in time of about 250 hours with those Muse capacitors.