Hi everyone.
Small update - I have tested Serial port circuit and I think I found the issue - either EMI filters or C310-C316 capacitors are problem - I have tested new 1488 and 1489 chips and they didn't help, then I tried to short CIA pins according to Amiga Test Kit dongle schematic and then it showed pins as working, same with shorting Paula RX-TX pins.
With the kronos card in you can run SYSINFO and it should show under Devices what the scsi device name is.
then just set that in HDtoolbox icon info and it should scan it. if you want a better card with ide support you might try a BuddhaFlash
Thanks for tip, I will check it next time.
Hopefully you're only socketing the Commodore ICs, ROM, CPU. With none of the logic gates, etc, in sockets - which is just asking for trouble, especially if using second hand corroded ICs.
It's too late now. Every chip on my board is socketed

I will just have to deal with it, I tried to use mainly precision sockets (with round hole) but some chips have normal double spring sockets.