Good morning Nick,
Yes you will be able to use your seatime that you earn from the US Coast Guard and convert it to a merchant mariner licenses or endorsement. We specialize in this at Mid-Atlantic Maritime Academy. According to the Marine Safety Manual Volume III Bosn Mate, Operations Specialist, Gunners Mate, Quartermaster, and radarman are all acceptable rates. When you submit your application to the Coast Guard they will only accept 60% of the sea time. All of your sea time must be over 200 gross tons and 50% of that must be on vessels greater than 1600 gross tons. Your best bet is to get on large USCG Cutters to satisfy this requirement. While you are in the coast guard I strongly recommend that you either take the AB course or schedule to go to the REC and sit for the test. You can advance your endorsements/licenses while on active duty. If you get the chance to get our JOD or OOD do it. These will only help you qualify for 3rd mate.
As far as STCW is concerned there are various requirements per level.
Basic Safety Training can be satisfied with your boot camp training as long as you can show 360 days of sea service every 5 years since boot camp. The only portion you will have to complete is the immersion suit training. All this requires is for to show that you can get into an immersion suit in a specific time and enter the water correctly.
Rating Forming Part of a Navigational Watch (RFPNW): This is your helmsman and lookout training. You must document your PQS’s demonstrating your proficiencies in these areas.
For 3rd mate there are a series of courses that you will need to take, anything from original radar to terrestrial & coast navigation to meteorology. There are 15 courses total. The good news is that your GI bill and TA will be able to cover these classes.
I hope this helps. Feel free to e-mail me if you need further guidance. Good luck and following seas!