First of all, congratulations.
The Middle Fork is maybe the best trip you could take in the lower 48. I've never done it, but know lots who have - had a permit last year for early season, but the river exploded - twice normal level, and we had to bag the trip - too dangerous.
And that's the key to your questions. When is your launch window? Because that will determine everything from where you put in and how your shuttle is to what the river is like. In the early season, you may need an airplane shuttle because roads are snowed in, or you may have to put in on Marsh Creek near Stanley and run that to get to the middle fork.
Get online - maybe try IOGA.org, and pick an outfitter that runs the Middle Fork. Call them up and they'll have info for you - most of them are pretty cool.