Instead fixed resistor R1 is better to use trimmer variable resistor of 2-2.5KB - so can adjust timings better.  Monostable delay should be around 180 nS. But it depends from used GAL delays and CF card too.
  If want to connect 2 CF cards need 2 CF sockets. In that case pin 39 of Slave socket must be left unconnected. Instead CF socket may use IDE connector + IDE-CF adapter. Connections should be obvious :  then no A03-A10, /ATASEL, /CSEL, /WE, /VS1 .  /REG is /DMACK on IDE & /INPACK is DMARQ on IDE .  Possible problem:  some IDE-CF adapters have unconnected DMA lines - in that case (of course) fast DMA transfer will not work !
  IMP DMA chip in Mega ST :   On chip is printed: 
    IMP
 C100110-001
© ATARI 1987
-31 I10354-01
9022 PAF  or   885 1DKA   ( year 90  or 88 ) .
  With such chips I observed problems only in Mega ST - unreliable work, even in slow mode. In 1040 ST it worked well. Is problem in bad cowork with blitter (what is not present in 1040) or not, I can not say. In any case, replacing IMP DMA with 'regular' one solves problems. As regular DMA chip I consider:  CO25913-38  .

  Decoupling ceramic capacitors (100-220nF) on all chips are mandatory, especially on GAL - best to solder on top of it.
 
 If adapter is connected to ST, and no card inserted it will block floppy controller - so remove adapter in such case. Same is when no Master, just Slave inserted.

GAL logic (GAL+JED files)


 
PP, Sept. 2010. June 2011