the 15pf cap stops any dc component upsetting the console, it does block the dc, but the chip looks for a change in state i.e. a switch rather than a voltage etc. 90% of the consoles I have done have been using a 15pf cap.
Putting a cap across the resonator will stop it resonating, as the cap effectively short circuits the oscillations. Not a single one of my installs has had a resistor across the resonator, although the sx datasheet does specify 10k ohms for that type of res.
All i can suggest is to recheck all your points and perhaps shorten the wires to the bios chip (mnop etc.)
The clicking problem sounds like you may have a partial short or some flux on the controller chip.
recheck all the cdvd points and expecially between them
NTSC/J 15000 Messiah 2 pro 1.30
PAL v3 30003 Magic ICE
PAL v5 30003R Magic ICE
PAL v5 30003R DMS3
PAL v7 39003 Magic ICE
PAL v9 50003 Messiah 2 pro 1.31
PAL v4 NEO 4 plus booster
PAL v12 Crystal Chipped + Diode mod