I'm wondering if the solder I have is the problem, I have heard some people saying that newer lead free solder can be extremely difficult to work with.
1) Always keep your sponge wet
I have a flux pen but if I'm honest I don't know how and when it should be used.
the iron is on the parts so long that they start to melt
Anyway your jaw will drop the first time you see solder flow after application of flux.