Glad it's working better now.
For your -12.4V problem, that circuit is pretty simple. A 6.2V Zener drops Common down to -6.2V which also goes to the + input of an op-amp. When things are working correctly, the -12.4V is divided by two equal resistors such that -6.2V appears on the - input of the op-amp. The whole regulation of the circuit via Q11 and Q12 is achieved because the op-amp tries to adjust things so that + and - inputs are equal, i.e. produces -12.4V.
If you are getting something other than -12.4V, two things could be wrong. The first is that the Zener is no longer behaving like a 6.2V Zener. But you said earlier that you measured -6.25, so that's not it. The second thing is that the two divider resistors are incorrect. And where are those resistors? Z1, of course! So you might check those Z1-J and Z1-K. Wouldn't surprise me if they have changed values given your other problem with Z1. A larger value for Z1-K than Z1-J would make the -12.4V drop down more negative like you are seeing.
As far as the current limiting, I assume you have already tried to adjust the two pots and still couldn't get to 550 ma. Note that the current adjustment pots are both in series with 30K resistors. And where are those resistors? Z1, of course! The current limit (-20V as an example) compares the voltage after the current sensing resistor, R28, to a reference voltage set by R26 and Z1-N. If Z1-N has increased in value, then R26 will run out of room and not be able to get to the voltage that you would need when 550ma is across R28.
Seems to be a common thread here. Also note that the two current limiting resistors, Z1-D and Z1-N, as well as Z1-K in the -12.4V circuit all share a common pin 5. If there were some added internal resistance on Z1 pin 5, that would explain both of your problems.
On my unit, I could easily set the current limit to 600 ma on both +20 and -20V supplies. I didn't go any higher than that because that's full scale on the meter. But I would guess I could have pushed it somewhat higher.