Most direct route from Pamplona to Burgos

While it is not "a walk in the park," keep at it within your constraints. Sometimes The Forum enthusiasm makes it sound too easy. Crossing the Pyrenees takes on an aura that ignores the several days of pain that can result. Starting in Pamplona avoids a bit of that. There still is plenty of challenge, but of a gentler sort, and a lot more stopping places than in Stage One from SJPdP. I suppose it is too late for that idea to help you.

Rest days have amazing restorative powers, so give your muscles and joints time to recover by alternating walking days for a while. Buen camino!

It's a decent pull out of Burgos before you get to the Meseta.

I think it is a good decision. I don't know when and why SJPP became ·"the official starting point", but yours could be anywhere you want.
The Mostelares high, after Castrojeriz, is tough to climb up, but after that, there is not a descent, but the beginning of Meseta proper. If you have some problems with Mostelares, you can go the way preferred by cylists, that is, to Castrillo and then rejoin the path in Itero. It is a local road, with little traffic. But it is a detour, and it could be lonely. There are quite ups and downs later, in Galicia, but I am sure your body will be by then adjusted to the stress.
Buen camino (from a fellow pilgrim also with a bad knee...