if it was me doing it, I would leave boiler pump, motorised valves all wired as is, leave cyl thermostat wired as is, leave LN&E supply as is and remove everything else and wire the nest in, easy job when you have done it a few times, hate trying to follow others wiring, and remember colours mean nothing, although yours looks like it has been pretty well done using sleeving to indicate wiring functions, if you do that all you need is LN&E connected between the two, SL from CH on and HW on to corrosponding Browns on the zone valves then T1 & T2 connected at each end, simple as that , you might still need to link out the existing room thermostat , just removing it will leave an open circuit