1.4 to 1.8 k series conversion problem

We have just finished fitting a 1.8 to my 1.4 rover 214 bubble, we fired it up and it ran but its really lumpy it judders, its misfiring and sounds generally rough, so we left it thinking the lifters are a bit funny due to not cleaning them out before fitting, but every time we return to it after about an hour or 2 its still the same, by the way this is a freshly built 1.8 that's been reconstructed down to every nut and bolt, any help will be much appreciated as I want to kill it!!!

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