I'd probably the problem areas for now as they look pretty minor.
The small knot on the belly can maybe be picked out if there is loose stuff, but no point until after heat treat.
Yes, with heat treating, get it flexing to maybe half draw first.
Put the middle in the middle, don't over think it or just ignore the 1" difference... it hardly matters on a bow that long.
Similarly don't define which limb is which until it's 90% finished. I've flipped several bows quite late in the build, and some have been flipped one way then back again.
I once had Robert Hardy tell me by bow was 'upside down' because the lower limb looked weak. I popped off the string and showed him it was just natural deflex... you can make up your own mind. But bear in mind the lower limb is usually a bit shorter and thus it has to bend tighter, if it starts reflexed relative to the top limb, then it's having to bend even tighter still. So my bow may have look odd, but the lower limb wasn't over stressed.
If you want to match the limbs a bit better, then during heat treat, you could take out the slight reflex, or add a bit to the other limb.
Del