Hey Scott,
1)what tool do I use to gap my valves?"
Motion Pro or your Honda dealer sell a valve clearance tool - feeler gauges - bent at each end - one end has 0.002 (intake) and other end has 0.003 (exhaust) -they also have 0.004/0.005 (use the 0.004 to make sure the gap is not too wide). You can also use feeler gauges bought at any auto store as long as they have the correct size gauge (see the above numbers).
2) should I check my chain while I am looking at the valves.
Camchain? Yes thats part of the tune up. Take off your points cover (lowe right hand side) - use a large wrench to rotate the engine (clockwise) to 15 degrees past TDC at the 1-4 marks on your timing plate - there is a small gap for you to look through to see the marks on the timing plate - your manual will also show a picture of this. Once at the correct position look at the back of your engine and you will see the camchain adjuster and locknut (refer to manual for pic) - loosen locknut, loosen adjuster nut and then retighten. Thats the camchain set (unless its stuck in which case you use a screwdriver to push gently on it through the back of the adjuster unit).
3) Is bench syncing my carbs effective enough to make sure the engine is ok( I know its not the best)
If done correctly should be ok for now. You can also check your plugs to make sure all look the same. If one is sooty and the other white you know you are running unevenly.
4) The mechanic that I took the bike to put plugs with resistors on them... should I change them out before doing any of the other tune up stuff?
Replace with NGK D8EA non-resistor type (assuming stock coils/caps). Starting with fresh plugs can make all the difference.
5) Is there anything else I should be looking at before I hit the carbs again? Or should I hit the carbs first?
Do the above first and then see how it runs. One thing at a time.
Good luck,
Andy