I didn't know where to put these two questions, but container citrus will do.
First question was partly because of a comment from Babyblue.

1. If a twig starts dying back for any reason, do you cut it off leaving a bit of dead wood, or always cut into healthy green growth?

2. When you have a budded plant starting to grow, do you leave a 1" stub of the rootstock? (I know some commercial nurseries do), or do you cut the rootstock off flush?

Good questions Mike. Here's what I do.

1. I cut back to just above the next healthy bud,

2. To force the bud I cut about an inch above. Once the bud has flush out & is healthy I cut almost flush. Cutting flush will let the wound callus over and be almost invisible in a year or two.

1. Cut back to healthy green growth.

2. Leave a 1/2" stub.

I can only answer for #1 when the problem is a disease like sooty canker (Hendersonula wilt)-- the recommendation is to cut back at least 12 inches below the lowest sign of the disease.

I had to do that for my ponkan mandarin, but it came back strong after the severe pruning.

Skeet

I cut the dead branch portion back to green wood. If the branch is dying due to disease I cut back even further.

I leave a 1/2 inch stub, then do exactly as Laaz states in his thread above.
Millet