As long as you piece of wood is not completely surrounded by the adjoining piece , you can resaw it by running a #3 ur between them! google resawing with a scroll saw.. I believe Steve Good and Judy Roberts have tutorials on this technique!
as far as glue bottles go , find a supplier with interchangeable tips, I use Stick Fast medium gel ! It's available on amazon They have about the best system out there with interchangeable tips!
As far as fit goes, be sure you are letting your blade do its job, take twice as long to cut you will be done faster and twice as happy with your work! Enjoy your time behind the saw, it's a wonderful process, not a race!