Pipework Mix Up?

Hi there I recently relocated some pipework so that I could fit more ceiling joists to reinforce our loft conversion to meet building regulations. Anyway along the line something has got mixed up or at least I think it has. There are three pipes one from the loft space which does not connect to the cold water feed or expansion tanks looks as if it is coming from the boiler returning the cold water fed into it hot, the other pipe goes into the bottom of the hot water coil in the hot water cylinder the third comes from the three way motorized valve and thus connects to the top of the coil, a feed from the loft with a pump on which has not been touch and the third pipe in question. I have had the pipes connected in numberous ways ranging from the suspected boiler feed only feeding the bottom of the cylinder coil which links anyway to the three way valve thus supplying a circuit to all three being connected. Another couple of pieces of information is that two pipes where connected by a manafold probably for airing or reliefing pressure from the system and the second piece of information that may help is no matter how i have the pipework it seems the pump is pumping various amounts of water around the circuit and when the programmer is switched to on or high the boiler initally ingites before turning itself off my guess is it's overheating due to an air lock or incorrect piping you can hear the water initally filling the boiler as well as air pressure noises. It then will relight after cooling off and turning the programmer off and on but not hot water or central heating even though there is pressure at the radiators and taps. Please help we need Hot water, not so much heating at the moment as it's summer but hot water as a necessity for bathing etc. Thanks in advanced.