I think you have a couple of points of confusion on the timeline: you don't need a second blood test, just a health exam where the doctor will fill out the 998 form. And you can wait more than six months after the test/titer before having that exam, but it needs to be before the vaccine expires or you need another vaccine (but not the whole test again). After the 998 is certified by the USDA vet, it is good for four months.
If I were you, and you know that you will be working with this vet for the process, you might as well do the microchip and vaccination right now and have it be official. Otherwise, you will end up needing to do another rabies vaccination later. You will need a rabies certificate (which your vet always does) with the microchip number on it. I made sure that the microchip number was typed in next to my dog's name--my vet also attached a sticker with the number, but I didn't want it to look like it had been added later. I think that would be the only piece of paperwork you would need at this point.
Is your vet USDA accredited? Not all of them are--apparently it is only useful for things like imports/exports and working with farm animals. There has been some discussion on this board about whether a USDA accredited vet is necessary for the whole process or just for the final certificate, but I would use one for the whole shebang. Your vet should know if s/he is USDA accredited. If not, call around--I found the USDA office unbelievably unhelpful in finding me a USDA accredited vet.
Hope that helps, and isn't too confusing. I should give the disclaimer that I'm in the midst of doing PETS--my animals haven't made it through yet. But we've done the rabies and the titer, and we're just waiting the six months now. My vet looks at me with fear in his eyes when I walk in (I've been a little nutty about the paperwork. . .), but otherwise so far so good.