Right, Somehow I have managed to make it work more or less stable... I am still getting the multiple entries in the boot menu but I believe Piri is right - it could be normal.
After rearranging the sims on the CyberStorm I have managed to find a positioning where they actually work together (2 pairs of 16MB each, totaling 64MB on MK3) then have also managed to find 4x4MB that worked together and put them into the mobo. I am not sure what could cause it but after about 20-30 reboots and mem tests the whole system ran stable for an hour or so. (DOPUS filling the memory, session of SlamTilt, filling the Ramdisk with files, and copying them back to the HDD. System booted from SCSI drives as previously with clean OS 3.1 installed. Eventually I have put the Micronik daughter board in, filled all the slots with the cards I had and basically continued to test. Again after a painful process of putting one card at a time, booting the whole system up playing with dopus filling the Ramdisk and then restarting without startup-sequence to test the memory the whole thing seems to be stable! Then I have measured the voltage.
+12V measured to be 11.5V and the +5V measured to be 4.9V (after booting with all the cards and the CV PPC in). SCSI drives seemed to drain approximately 0.2V on the +12V rail as without them the total voltage raised to 11.7V and 5V. -12V seemed to be always the same = -11V
Taking all the cards out (except for the Scandoubler and CV PPC) resulted in (sic!) raising the voltage to +11.6V, +4.9V. Then I have connected another ATA drive (old power hungry Maxtor) and that seemed to overload the PSU as the Amiga did not boot at all (although the voltage only dropped to +11.4V +4.85V) but when I pressed the reset button the meter went nuts - measuring tops of +3V on the +12V rail - without the maxtor - Amiga still seems to be stable. Although I think missing 0.5V on +12V rail and 0.1V on +5 might be the edge for this configuration. I will look into a new PSU soon but for now it seems to work? Although I still haven't installed any software, did not play with it for more than an hour. So rearranging the cards, assembling the whole thing properly (all the screws, etc), pressing all the chips across the mobo and the expansion cards seemed to help for now. I will get a new PSU, new battery and post more results later on when I find a free day to play with my "new" toy

Well - thank you all for your help - it looks like we've nailed it!
kind regards
tinner.