Fried Alternator?

So I am finishing up an engine swap, and yesterday I was priming the oil pump before firing it up. I was cranking it over before I connected the spark plugs, and after I was done I noticed there was an electrical smell coming from the alternator. After connecting the spark plugs I noticed that starting it up the alternator was not charging.. I traced back the electrical connections and I noticed the ground between the engine block and negative terminal. Question is would cranking it over to prime the pump and testing the timing with out the negative ground to engine block fry the alternator?

should not have, get it running & check alt output with meter & get that ground hooked up

The ground is hooked up now, and I had it running but the voltage gauge never went above the residue in the battery..

Could the B+ terminal and the ground to the ignition coil wires be swapped and cause that?