Can I remove the CDR valve components and replace them with an air breather/filter? If I do are there any potential problems. I read the archived section on the CDR valve system but it did not say whether or not you could remove the components and what, if any, the negative side effects would be.

No you can not, the CDR is designed to regulate crankcase vacuum, it you completely remove it or vent it to the atmosphere, you are completely defeating the purpose of it and have a greater chance of causing oil leaks.

I know what you are thinking. I just turboed my 6.2 and tried to put another breather on it. NO luck!!!! with in just a min or two of running the engine with a breather, oil came out the top of the dip stick and out the rear main seal. so stick the the cdr valve. Lots less problems and money saved..