Under $1000 each component used. What would it be ?

OK, I'll take a shot.  I am limiting to components with which I have had personal experience, a number of which I currently own, (including the Ayre, the Truth, all the cables, and the Shelter), or have previously owned.  I include both a full function preamp and a line / phono combination, but at this price range, I see no reason to go for a standalone phono option, particularly given the need for an additional IC - I think you are far better off getting a full function preamp.  Also, $1k for speaker cables / ICs seems disproportionately high in terms of the overall budget - spend less on the cables and more on the components.

Amp - Ayre V3-X
Preamp (Line and Phono, $2k) - CAT SL-1 Signature
Preamp (Line, $1k) - The Truth (Hornshoppe)
Preamp (Phono, $1k) - Pass Labs Aleph Ono
Speaker - Ariel 10t, Thiel CS 3.6, or Avalon Arcus
Interconnects / Speaker cables - KS Emotion (if short lengths), Silversmith Silver, Wireworld Gold Eclipse III or later (if longer) 
Turntable - Technics SP-10 Mk II
Tonearm - SME IV
Cartridge - Shelter 90X

Looks good. Are there respectable tube phono stages under $1k?

Here is something quite different.

Turntable - Nottingham Spacedeck
Tonearm - Nottingham Spacearm
Cartridge - Any MM of your choice except Grado, Ortofon, Shelter or Clearaudio.
Phono stage - AcousTech, designed by Ron Sutherland.
Integrated amp - Gryphon Tabu or Gryphon Callisto 100. I have not heard Gryphons but read enough. This would be my educated guess.
Speakers - Dynaudio Contour 3.
Cables and power cords - Purist Audio Dominus interconnect and power cords, Proteus speaker.
PS Audio Premier Regenerator for turntable and phono stage, maybe for Gryphon too but that I am not sure of.

Alternatively. Rowland Concentra I integrated and Vienna Beethoven speakers.