This is the basic idea of my stair layout and what I want to do. First 9 steps are open on the left and last 6 steps are closed on both sides.

I've got the treads and risers installed, and it's time for the handrails and balusters. The instructions I've found on the web for installing wrought iron balusters all assume a remodel, keeping the existing railing and just swapping out the balusters. That way you've already got aligned holes and it's a relative piece of cake.

What I need help with:
1. How do I cut the handrail so it's got the right angle between the top wall and the bottom newel post? Do I lay the bannister along the front edges of the treads, use that as my angle, and then just raise it up 34-38" and attach it to the wall and newel? Easier way?
2. How do I align the holes in the treads and bannister? Can I install the bannister first, then drill the hole in the tread, use a level to make it plumb into the top, and then use a jig spacer from there? Easier way?
3. I need flat shoes to cover the holes in the treads. What about the holes in the underside of the bannister? You can buy angled shoes, but they are 45 degrees, and my bannister won't be at exactly a 45 degree angle. Do I omit shoes on the top? If so, how do I cover the ugly hole/epoxy?
4. On the upper (closed) portion of the stairs, the PO never installed a handrail. The easiest fix would be to add a wall portion with returns on top and bottom. But in reading the stair code, I think I am supposed to make the whole thing continuous, i.e., jog the handrail in when it hits the wall, then continue it on up to the top. Can I get away with a discontinuous one? I'm having a hard time envisioning how the balusters would work if I did the bendy one (i.e., can I maintain the <4" opening?)