Hi @Steven_Hansen,
This topic was discussed here also…
Circumvent Revit Object "replacement"
It seems to be common issue. But, I can see a very good reason why Dynamo should keep track of elements it creates (Element Binding). There are ways to get around it however, Python works for me as the Element Binding does not happen, so a solution is to either code your own, or use another 3rd party package (like clockwork or rhythm etc - I do not know if they have a node that you are after, just saying that if they did then they would work, have a look, if you can’t find one, post back and maybe one of us Python guys will knock one up real quick 
)
As for code blocks, this is interesting that you can circumvent Element Binding this way, pretty useful to know. Have you tried creating the script out of the Nodes first then selecting them, right clicking and selecting the “Node to Code” feature. This will convert the nodes to Code Blocks all ported correctly and ready to run.
Also, just for completeness, when you have those yellow errors, could you specify what it is saying, my eyesight is terrible 
Cheers,
Dan