Version 1.5 of Atari ST ATX
All small mistkes fixed, everything works fine. There are two jumpers, now You can chose which TOS (1.04 / 2.06) You want to use.
IDE works good, ACSI also works good.
STGA1040 working on Atari ST ATX motherboard

Eagle files and gerbers:
AtariST microATX.sch
AtariST microATX.brd
gerbers.zip
iBOM: iBOM.zip
BOM: BOM.csv
BIN, ROM, JED and other:
IC10 Eiffel
IC11 IDE + TOS logic
IC12 STGA1040 logic (thanks to Idek)
IC32 TOS HI
IC31 TOS LO
For STGA1040 I'm using STGA_ET4000T3_V301.zip driver from https://silicon-heaven.org/atari/nova/ST - MegaST/STGA/
Local mirror:
STGA_ET4000T0_V301.zip for DAC TR9C1710 8-bit
STGA_ET4000T3_V301.zip for DAC KDA0476 8-bit
STGA_ET4000T6_V301.zip for DAC SC11486CN-66 15-bit
STGA_ET4000T8_V301.zip for DAC W82C490 24-bit (?)
I was informed, that order of driver files in AUTO folder on CF card is very important. You have to put them one after another: first one is Emulator.prg then Menu.prg/Xmenu.prg and then Sta_vdi.prg and then rest of them.
My ET4000 model is:

Some pdf files:
AtariST microATX sch 1.pdf
AtariST microATX sch 2.pdf
AtariST microATX sch 3.pdf
AtariST microATX pcb top.pdf
AtariST microATX pcb bottom.pdf
AtariST microATX pcb top+bottom.pdf
AtariST microATX pcb top+bottom rastnet.pdf
AtariST microATX pcb parts top.pdf
AtariST microATX pcb parts bottom.pdf
AtariST microATX pcb parts top+bottom.pdf