I have not made this kit or style of beer.
I would add in 1/2 the extract, boil, add hops then at flame out add the other 1/2 of the extract. You REALLY have a lesser chance of caramelizing the LME this way.
Clear bottles are fine, I did read a few threads that the brewer did use clear bottles and left them in direct sunlight for 2-10 minutes to intentionally skunk them, if you want that aspect to it as well. It is easy to ad skunk by exposing the bottles to direct sunlight but impossible to unskunk them if they get "over skunked".
“I'm not drunk, I'm from Wisconsin.”
We have been out drinking your state since 1848!