Well, he didn't use 13s. That's a myth that's been debunked time and again. He used 11s, but switched out both e strings to the ones from a set 13. But he would also frequently start with lower gauges at the beginning of a tour, and then work his way up to "his" gauges. And he would often go down on the high e (13) string to a lower gauge if his finger were getting sore. So that he ever used a straight set of 13s is just caca, but I digress.
I would alternate pick most of it, regardless if I start on an upstroke or a downstroke. If you play it all slides (like I did on acoustic earlier today), I would pick the a note on the g string, and then slide up to the b note, and the pick the open b string. So 2 plucks, both in opposite direction.
I would only do two upstroke in a row, if I started the lick on a downstroke. When doing that, the little flat five slide and pull off thing on the g string becomes an upstroke, and I want to e on the d string to be a upstroke as well, so that the low E on the 1 of the next bar ends up being a downstroke. Theoretically, starting the lick on an upstroke is more in time, because the first open b string lands on 2 and becomes a downstroke in that case. It may not be the most economical, though, depending on how you play the rhythm part leading into the lick. I'm a firm believer in keeping time with the right hand, so the low E in the rhythm part goes down-up-down for me, which might be awkward for some people.