Take a PDF, copy all, paste it into a .rtf document in textedit, --> make plain text. will this remove/nullify any malware from/in the pdf? In other words, if I open the PDF on one machine and convert it to plain text as such and then send the plain text file to a new machine, the new machine will not be at risk?
As soon as you open the pdf to copy its contents and if there is any exploit present then it is going to be executed if your pdf reader is vulnerable to arbitrary code execution vulnerability and then it will infect all your files or just open up a backdoor.
If you want to open such pdf files create a virtual machine using vmware workstation put the pdf in a virtual machine and open it with updated pdf reader like adobe reader then you can copy and paste the contents of pdf file in a guest machine (virtual machine) to a text file in a host machine.
If you copy the (text) contents of pdf into a txt file then the malware won't work.
Saying that a file is malicious or not has nothing to do with its extension. Rather the application with which it is opened will be the vector of the malware that is emebded within the file or not, depending if this application suffers from the vulnerability the malware is targetting.
When you open a PDF file, you are going to be infected if your Acrobate Reader (check the security bulletin) version is vulnerable to the malicious content the file embeds, in which case your question does not make a sense.
But if you mean if the operation of savng just the plain text of your PDF file into an other file with a different extension will or not remove the malware from your PDF file then the answer is (absolutely) NO. But if you mean if the produced file in which you copied the plain text is safe or not, then it can infected too especially if you have on your computer malware that is listening to COP/PAST events or to its equivalent functions and triggers malicious activities on your computer that can have different impacts.