Should you keep pressing with the routine, even if it means waking him after he's only been asleep a very short while?
I would say yes just b/c that is what I believe. Now, there is no harm in giving him another extra 30 mins, but I wouldn't let him sleep past an entire feeding time. Tracy says to work on the nap for 40 mins or until the next feeding time, give the feed, and then work on getting the nap again right away or very soon. Sometimes, however, you both need a break and you shouldn't feel like you have to spend hours in a row working on naps.
What do you do when he takes so long to go down between feeds that he actually doesn't go to sleep at all?!
This would be the same as above. What methods are you using to help him fall asleep? Do you have a winddown, swaddle, use white noise? Remember, after you do the winddown, you put him in his crib. You don't have do use shh/pat unless he starts to cry hard. You should give him ample time to settle himself, and only use shh/pat if he is crying an "I need you now" cry. Fussing and whimpering are more of the "mantra", settling cries than an urgent cry.
Should you keep trying to settle your baby when he seems very wide awake and alert, even if he hasn't had much sleep?
If you know it is time for a nap, but he actually looks wide awake and alert, he may be overtired and running on adrenaline. Spirited babies tend to look this way the most when tired, and having set naps times can alleviate the confusion usually. You could put him down and walk out of sight for a few minutes and see what he does. Also, you should make sure to hide any visual stimulations, making the room as dark as possible, too.
How long should you sit in the nursery trying to settle him?
I think Tracy recommended working on the nap for 40 mins or until the next feeding, which ever comes first, then take a break. Come out of the nursery, but keep a very low-key environment. Remember, this is supposed to be naptime, so activity should be extremely limited. Perhaps keep the lights dim and speak softly. Or, just sit with him listening to light music.