I believe when I ordered my master kit from them, the bearings where included "at the time". That would be 6 total, 2 on the input shaft, 2 on the output shaft, and 2 on the diff. All 4 seals were in that kit as well, and they're the better seals. The shift shaft seal had the metal lip that catches the edge of the rubber bellows, and the axle seals had that extra extended "dirt rejection lip" on them, which is impossible to get at auto parts stores. You're right about the syncros being seperate though. You can do this job with basic tools, and a gear puller.
For some reason, and this is important, guys get stupid when it comes to removing the bearing on the diff carrier that faces the plastic speedo gear. They try to get the puller in there gently, and then can't get a grip, and then go and trash the speedo gear. Duh!, you're throwing the old bearing away! Trash the old cage, and then grab the bearing at the race lip with the puller, nowhere near the ever-so-rare, almost unreplaceable plastic drive gear! Check with them about the bearing count, the kit may be different now, they're easy to deal with.
By the way, I have a ford factory cd manual that shows how to completely disassemble and reassemble that transaxle...pm me for details. Good luck