I am not sure I received Kelly's private message nor a notification with the latest message in October, sorry! Kelly, if you are still following this thread of messages and still need help, please send your files so that I can check again.
Skip, your tree file has branch lengths and the notation that you are using for the calibrations is incorrect (i.e., wrong format). In a nutshell, you have soft-bound calibrations following this format: "B-2.356-2.631-9.99999999999999e-301-0.025-". You should follow the format "B(min_age,max_age,min_tail,max_tail)". For hard bounds, please use "1E-300" -- not sure what "9.99999999999999e-301" is supposed to mean. I have seen that you also have lower bounds, which also follow the wrong format. You can find all the details regarding the PAML notation to incorporate node age constraints in
the PAML documentation (pp. 49-52). As aforementioned, please also remove the branch lengths as detailed in
the PAML Wiki too. Seeing that you have formatting issues in your input files, please check that your input sequence file is correctly formatted -- you will also find all this information in the PAML Wiki.