Replace C28 with... ?

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.