The volume of water in the loft tank shouldn't be any different because the tank has been lowered. Is your issue, with the shower, such that you run out of hot water ( goes cold) or it runs out of water completely?
The silver coloured braided hose in your picture ,under the boiler, is what you connect to the two filling loop valves . As above ,you need to remove the chrome caps first.
Very unlikely that a 4 inch flexible waste pipe would suffer from limescale build up. More likely a physical item. Did you ever use those hook on plastic things that hang over the toilet bowl and hold those things that colour the water ? Any kids in the house that may have dropped something in...
I can only guess that the previous owner turned off all the radiators by their TRV ( or wheeled valves if no TRV) during summer.
If you run only central heating on the programmer,does the hot water cylinder also heat up ?
So you have a 3 port motorised valve ,is the brass body and actuator head all brand new ?
If so ,and the pipe from the valve to radiators isn't hot,then there must be reverse circulation taking place through the radiators
Check the supply pipes to the tap , particularly if Flexi hose tap tails have been used ,which may be bent/ twisted restricting flow.
If isolation valves are fitted to the taps supply pipes ,are they fully open ?
The cleanser needs to run around the whole system, for a few days minimally.
Is water coming out the vent pipe ,and into the f&e
When system is running ?
Is the feed from the F&E 22mm ? Is there a seperate vent pipe that comes over the top of the F&E ?
Did you check the copper TEE next to the compression T ?
I would add a chemical cleanser to the system.
Sounds like a good plan ,but I would also drain some water out so it's at a lower level than the Tee, otherwise you will have to contend with water leaking out when opening up the compression Tee.
I think it's unlikely that the gate valve is blocked with sludge / magnetite.
What do you mean by it's spinning freely ?
It should come to a stop when it reaches its closed, or fully open positions.
If it spins freely continually ,that's a problem.
Possibly blocked,or partially at least.
If you have a strong magnet run it around the Tee in the Copper pipe,the pipes and compression Tee.
Any blockage ,or build up, of magnetite will attract the magnet.