Hard to start when cold

And it started and ran fine prior to the change? Just eliminating and narrowing down what could.

So when you did the chain are you 100% sure the #1 piston was at TDC and the balancer pointer was pointing to "0"
Honestly I am not sure again this is a lot of stuff I am not familar with I will ask my father however I will provide a picture of what it did look like when we put the gears in. This picture is just off the internet I am using it as an example where the two marks lined up like this

IMG_0177.jpeg