It really looks like you have no sync at all getting to the monitor ( horizontal or vertical), the pinouts you describe are correct for the new chassis you have as long as you have them connected that way and havent made an error.. You can try adding the vertical sync but it really should not be needed unless this chassis has an issue with some composite sync signals. If you do try the vertical sync you should cut the trace on your amp board so they become separate.. Also some chassis have a sync select switch on them, im not sure about the chassis you have but see if there is one on the chassis..

Can you take a picture of your connections ( video) both ends from amp to chassis? And you did confirm the 5volts you connected is there and correct?

No need to discharge the monitor, the part your working on is isolated from the High Voltage, the only time you need to discharge is when your removing the chassis completely from the tube..

If you still have it you should use the old video lead from the original chassis, do not use the AMP, make all the connections and see what you get..
Just slowly wiggle the connector back and forth or use a flat screwdriver to pry it if your having trouble..