I think this organ normally has a spring reverb, so one of the transformers and one of the 12AU7 tubes is probably for the spring reverb. I'd look to see where there is an Out and In connection (or a four prong) for the spring reverb.
With two power tubes (the 6L6s) you will need a PI tube but it could be one of the 12AU7s or one of the 12AX7s. I would look for one of the 12A?7 tubes that has direct connections to passive components that are then connected to the 6L6 tubes. The input side of that tube is the entry point to the power amp.
Why would you want to bypass the pre-amp? Does your daughter's keyboard not require a pre-amp? Or does it have line-level out?
I think I would at least incorporate the volume control from this amp so you can control the volume of the amp directly. It should be a power either connected directly to the input of the PI (Phase Inverter) tube or connected to a resistor that is connected to the PI input.
Hope that helps.
Have you got any pictures of the amp with the tubes in?