From your voltage testing, it looks like the 24VAC -> 5V conversion and 5V -> 3.3V conversion have failed, This could be caused by any of a number of potential issues, including whether diodes D1, D2, and inductor L1 are soldered correctly, MC34063 inserted correctly, and also the 24VAC transformer outputs a voltage that’s over-spec. I suspect the MC34063 switching regulator and MCP1700-33 linear regulator are damaged. Hopefully you haven’t inserted the other ICs and the LCD — in which case MC34063 and MCP1700-33 are the only ICs you need to replace. In case you have inserted everything, I am afraid the DS1307 and the LCD are also damaged, which you need to replace as well. Do please check your 24VAC transformer output before any further experiment.