Thanks, the picture is getting clearer.  How though could Sysex data get into a drum MIDI track inside Sonar that I created (hand-tabbed), and which is only driving a soft synth plug-in?   This is the part I'm not quite following yet....wouldn't Sonar be the only culprit in generating any Sysex data in that scenario?  And if so why would Sonar do such a thing? 
 
Sonic

If you're "hand-tabbing", and which is only driving a soft synth plug-in, then it's unlikely SYSEX is being injected into Sonar during this process and therefore SYSEX is not the culprit in this instance.  You need to look elsewhere. 

You might want to start a new thread with the title "Play back of MIDI events I created crashes Sonar" or something like that.  Then proceed to mention things like your OS and machine specs.  Which soft synth plug-in you're using.  Whether the soft synth plug-in is 32 bit or 64bit.

I was tackling your original question "Can MIDI (.mid) files have a virus"

Fair enough, makes sense.  
 
Thanks again for all the replies!
 
   Sonic