hi luke
had exactly same symptoms even down to head being refurbished not by us and popping back through inlet manifold when cold, after lots of testing we did a relative compression test using pico when cold, as missfire only happened for two/three minutes of starting from cold after that was ok, we found one cylinder down, removed head and found valve springs on that one cylinder had been compressed, presumably from belt letting go, replaced and happy days.
Not saying this is your fault but worth bearing in mind.

peter