The 3 port valve is just controlling the heating/hot water pumped circuits from the boiler, nothing to do with the shower circuit. Connecting 2x CWS tanks is not unusual to increase storage capacity but the inter-connection should ideally be 28mm. What size are the CWS tanks?
So you have a pump in the loft which only feeds the Aqualisa shower over the bath, what sort of shower is it? Was it a later addition to the bathroom or did the en-suite came along after? You say its cold water fed directly from the loft tank, does it not pump the hot water as well? What size/make/model is the pump?
It’s unusual to have 2 pumps so you may be able to utilise the one you’ve got depending on size & current pipe routes or you could replace it with a single pump with sufficient output for both showers, even if it means re-siting the pump.
Unless you have a pumped whole house system (which almost certainly you don't currently have), the shower HW circuit will always have a dedicated take off from the HW cylinder, either from a double outlet flange in the top of the cylinder or, preferably, a flange in the side of the cylinder, which do you have?
Lots of questions I know but unless you can understand a bit more about the system you currently have & how it’s all connected, it’s going to be nigh on impossible to advise; a bit like the blind leading the blind! If it’s not possible for you to make some sort of diagram of what you currently have, I would suggest you call in a specialist but be aware that “plumbers” don’t/won’t necessarily know how to design a pumped shower system so it will work correctly.
