Reasonable is in the eye of the beholder.  As Bob mentioned, the first question would be how much did they pay last year?  Sounds like you inherited a problem child.  Did the prior preparer have a big grin when he or she found out they weren't coming back?  I bill by the hour.  If I had that much time into the return I would bill it, but I would do a little of what you are doing as to second guessing if I would bill $300 for a similar return without the extra gymnastics.  If I thought the client was a nice person and just needed to do a little more learning on being prepared, I might ratchet the fee down a little.  If I thought the client was a pain in the neck, and not worth all of the effort, I would bill the $500 and not think twice.