Magic smoke is what makes the components work. If you let it out the components are dead. Some components on your sammichSID are now dead. Congratulations.
Do not power it up again until you know what's wrong.
Remove all ICs (SIDs, PIC, opto coupler, eeproms).
Remove the CS PCB.
Look for any traces of broken components (which left, btw? left as in west with the connectors facing north? oh and on which board? CS or vase?) or smoke residue. Find anything? Replace the part.
When all that is done and looks good, check ALL voltages again as described in the build guide. All 5V good? Voltage for the SIDs good?
Check the components around the backlight circuit next, make sure you got the right values in the right places (R3, R4, R4A, P1, T1).
Report back.
And remember: If there's smoke, don't start guessing and power things up again. There's been smoke for a reason.