The idea I was getting at is that the best way to train pullups is to do them and add reps when you can. They don't transfer WELL. But of course there would be some improvement versus training nothing.
Pullups are part and parcel with the starting strength. The best thing to do is not to worry about how many reps you can do but to just do it and add when you can. They are really meant as an assistance in this program if you do row as your main movement. Otherwise you can alternate rows with pullups or just do pullups.
I can knock out a good 35 reps at once when I'm fresh and 20 when I'm tired and that is from training pullups (and not really for high reps). I use around 45 extra pounds for high rep sets and 60 to 75 for sets of 5. Trust me pulldowns would not have gotten me there although I'll admit that pullups have always been something I can do well.
Although pulldowns of course will add to you pullups the fact is that pullups do more for pulldowns than the other way around. IMO, it is always a mistake to turn to a machine (pulley) to train a free weight or bodyweight movement. Just do the pullups and keep doing them. If Rippetoe were on here he'd chew someone out for doing pulldowns
The way the program is written, when pullups/chinups are done for assistance is 3 sets to failure adding reps until you them up fairly high. You can be very patient and try to get them up to the 12 range or you can get them to 8 and add a little weight. You could then go back to bodyweight and add more reps if possible. In other words you can play with them a little but the bottom line is to progress.
I'll have to disagree with your characterization of momentum in pullups Scorcher. With pulldowns you can lean back and use the lower back to generate "momentum". With pullups you can't. In fact any momentum you generate is from pure power unless you do "kipping pullups" which is a whole other story.