From whom do I get references when my original advisor leaves academia?
Your current advisor's letters are killing you.  Do not ask him for any more letters.  Do not list him as a reference in your CV.  Don't walk; run.


  I will add here that I have a number of publications (>5) including single authored ones-which for my field is significant- as well as an excellent track record of funding and in presenting my research. 


In that case, you really should have no trouble finding enough other good references to overcome any concerns raised by not having a letter from either of your advisors.  Everyone reads advisor letters with a grain of salt anyway; strong letters from well-known senior researchers outside your home department have much bigger impact.

Of course, if anyone asks why your current advisor isn't writing you letters, you should answer honestly, but I think adding an explanatory note in advance is unnecessarily defensive.