My name is Jon and I can help you today.
It seems that when you are putting the cover onto the boiler the gas to air mixture is getting thrown off. And causing the flame and heat to go out.
Are you putting the flame cover on before the outer burner cover that has the glass window on it first?
if not, that could be the whole issue.
That first metal flame cover needs to be on first so that when the outer cover goes on it will not blow out the flame or create a back flow inside the boiler and gas valve area causing the flame to get weak or go out completely.
Now if you have put the cover on before the outer cover and still the heat and temp is weak please try adjusting the gas valve and temp on the vale way up. Almost as high as it goes. Sometimes the gas valve will get stuck and even though it says that it is on lets say c, or 140 degrees, it may be way less.
so adjust the temp higher and see if the flame gets bigger? if it does then adjust the flame and temp accordingly and check the temp of the water.
If that deosnt help please get back to me here and I will help you more.