What is the best system one can make under $5000

You'll get some good advice here. You might also get some sneers at a budget of $5000 (but not from me).

I think a lot of it depends on what your needs are and what you want to do with the system.

I think if I were starting over (with my needs) I would do a lot of research and find a good quality used system. I'm guessing the system I inherited was probably $20k when it was new, around 10 years or so ago. I bet you could pick it up for $5000 now, without a high end turntable though.

On the other hand, there is a US company that makes reasonably priced components that punch above their weight class. It is called Schiit. Even though it is probably considered mid-fi or even low-fi by those with $20k and up systems they seem to garner a certain amount of respect for their price vs quality ratio.

I can't help you with speakers except to say that I love my Aerial Acoustic 7B tower speakers and did not love comparable B&W tower speakers (the model number I have forgotten). 

You might start by listening to some speakers and get an idea of what you like and figure those first . Once you identify the type of speaker you're interested in it's easier to get some recomendations for other componets people use with that type of speaker .Another thing it is usually a little less expensive to look at integrated amps with a decent dac and phono stage you can always upgrade the dac and get a better phono later. 

ClearAudio or MoFi Table
Ortofon Bronze
Parks Audio Puffin Phono
NAD 3020 D integrated amp w DAC
Vanersteen 1ci or Magnepans....
wire it all with Audioquest or Bluejeans cables..

pretty amazing sound...