The engine is an unknown so there are a lot of variables we don't know about. First, I have never seen Lotus TC timing marks that line up perfectly. Second, the engine is an unknown. Shaved head, worn chain, different block, etc can all make a difference in where the timing marks line up.
What to do?
First look at the timing chain adjuster. All the way in? Chain and maybe sprockets are worn. It won't make much difference for your issue but it is an important wear item to check.
After that, it ran well when warm, really well by your description. So, if it ain't broke, don't fix it. Put it back where it was and enjoy it. It's normal for a high performance cam not to be happy at low speeds when cold. Some race grinds don't idle at all.
No good enough? Won't sleep nights? Then screw the marks and get a degree wheel and dial gauge and check and see what the valve timing actually is. Contact Isky for the specs and set it up as per their recommendations. Offset woodruff keys are available to make adjustments. I would assume someone makes vernier cam sprockets as well, if you are totally crazy.
On Maserati V8s and V6s, there are no timing marks. The sprockets are infinitely adjustable and you set everything up with a degree wheel and dial gauge. First you find TDC exactly and then you go from there. Funny thing from back in the day. The torque spec for the V6 sprockets was too low. Normally not an issue as you don't spend much time at the redline. However, people would go out and see what their top speed was. Long straight, flat out, inching higher and higher when "WOOF" the nut would loosen and bend all the valves. The spec was changed to hit the special spanner with a BFG until it doesn't move any more! No problems after that.