How would you upgrade my entry level system?

As someone else stated, for $5k I would just start over and sell your current equipment.  But, for an upgrade path and more conservative approach...

Since you already listen to ripped CDs (hopefully at full resolution), why upgrade the CD player? Save the money for other components. I would do the following:
(1) replace the Connect with a Bluesound Node 2i.  Good server and decent DAC (and you can always add an external DAC later). $500
(2) Get an entry level power condition from Furman or Audioquest.  $200 or so.This actually made a noticeable improvement in my modest, second system.
(3) Get a high-res subscription service like Tidal or Qoboz.

I would do this before anything amp or speaker related.  See how they sound with an improved front end before moving from there. 

Don't know what you're using but you might consider upgrading your power cables. 

Think of it like you're building a house. First, start with a solid foundation ie. room treatments (GIK or ASC) and vibration control (Herbies has affordable options). Next. address your incoming power ie. power cords (many options out there, buy used) and outlets ( also dedicated lines of possible). Doing these things will pay off in the long run no matter what gear you get in the future. Good listening. Jeff

Keep the Brio R, then use the $5k as follows: $2k on new on Teac nt505 dac/streamer (best streamer under $5k imo) and $3k on new or used speakers.

Speakers are such a personal choice. I’d look at Focal Aria 936, Spendor A4, Dynaudio Excite X? whichever model hits that price point.

Then subscribe to $20/mo Tidal or Amazon hifi or Qobuz. Good luck!!

note the Teac requires Ethernet connection (not WiFi). If you can’t do Ethernet at install location then disregard my recommendation 

It would be interesting to hear what decision you made and how you feel about it now.

If you’re still weighing up your options I’d say spend the whole amount on new loudspeakers, full bandwidth designs flat down to at least 40Hz if you have the bookshelf QRs. If you have the QR5 floorstanders then your question becomes a lot more difficult as then your system looks pretty good already. You won’t need to ever change your amp until you have speakers that can benefit from more than the 50 watts per channel the Brio R can deliver.

In any the easy answer for me is to suggest spending your money on whatever makes you want to listen to music more.

Remember, the most expensive system in the world is just another example of money gone up in smoke if you hardly ever feel like listening to it.