Hi all
1st off I'd like to say thanks for all the help so far, I know I'm a bit of a nightmare when it comes to this sort of stuff but it probably stems from the fact that I'm an engineer myself and I've seen 1st hand the dangers of messing about with stuff you don't fully understand!
Anyway, I have put an update below on the results of what you have recommended, it's a bit long winded but I tried to cover everything, again I'm very grateful for the time people have took to help me with this.
I tried what you recommended, I turned the bypass fully off and turned the cylinder valve down to 1 turn open. It seems that this worked, the boiler ran for 30+ mins without issue. During this time there was a noticeable rattling sound coming from the bypass gate valve. I also opened up the lock shield valves in the radiators that have been having issues. During this time the CH return pipe was hotter than it has been the hw return was cooler,the bypass was still hot but I suspect that this mightve been because I did run the system with the bypass open for the 1st 5-10 mins.
I then experimented a bit by opening the gate valve, within a few mins the boiler began cycling again. Although this is a limited test and I'd probably need to do it again to confirm things (it should be noted that my wife had ran a bath and used up the hot water in the cylinder so I suppose the fact that it was full of cold water would've prevented the return from heating quickly?)
I still have it in my head that this bypass is a safety related item, in don't fully understand why it's there to be honest as a direct link between flow and return right next to the boiler seems a strange idea to me. Since I am put the house most of the day and my wife and daughter are in here I decided to play it safe for now and take Agiles advice of leaving the gate bypass open by 1 turn, the rattling got worse at this level though so it is probably 1.5-2 turns open now, I'll see how the heating goes at this level. The other thing I noticed for a fair bit of noise coming from the cylinder once the room thermostat had reached temperature and the boiler had stopped, it was a sort of water bubbling/boiling noise.
I have also took hughs advice and am waiting on a quote for changing to a S plan system, I have also asked for a price to fit an automatic bypass valve as I assume this will solve my issue of wanting it to be closed normally but be open when required.