Issue 5 then

 Just to be sure, the pullup resistors are 4K7?

Yes.

It is need more wires and switches: build a multi-trubo system.
My machine can run on 4, 6, 7.12, 10 MHz speeds, can be selectable with switchs.

Which EXDOS card are you using?

For a higher CPU speed I recommend replace the old 74LS ICs to 74HCT, EPROM to fast CMOS one or Flash ROM, and if the WD are old 1770 then replace with 1772.
WD1772 PH 02-02 have a "enhanced digital data separation" then it is more reliable about disk reading.
And with 1772 chip can be used fast floppy step rates, then the drive will work faster and quiet.

Also a lot of games shown sync artifacts and, of course, the ones working fine run too fast

Try my Freescape ports like Castle Master, Total Eclipse and others. These games can always make use of the extra CPU speed. But the sound will only be correct at 4 and 6 MHz, above that the pitch will be too high.

These games can always make use of the extra CPU speed.

Also try the Race Ace: the computer cars are synchronized with the video interrupt, only your car got a super speed! 

Two 4 speed (4/6/7.12/10 MHz) machines for Prodatron:
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How CPU clock is switched? Can be controlled from software, or some kind of actual switch?

Ok then, another white spot for me: It seems designers of EP already thought about the "turbo", namely 6Mhz, as Dave can be configured for that to have timings intact. However I always felt it's not a good solution as softwares can have the bad habit to write  their thought-to-be-correct value to the corresponding Dave port. As far as I know, for other solution (like 7.12MHz, derived from ~14Mhz pixel clock of Nick, I suppose) do not have this problem and Dave can be left in its "usual" state (as it would be for 4Mhz machine) but still having the right timings for sound, etc. Is it true? Because if it's 7.12Mhz is much more useful and "compatible" (well, of course there can be other problems like software can require 4MHz CPU clock to work correctly, etc) than the 6MHz planned mode by the designers.