1) yes to calanders,
2) runs take up weeks, but I will be assigning spare days in those weeks to offset currently running downtimes. Eg, run takes two days, I add a day at each end for prep and recovery, and declare 3 downtime days free in that week. Actual downtime does not start until the next week block. These would be used on training times. I am doing this to give a bit of Time back to the thumping schedule I have planned.
3) yes, mission uptime is synchronized, downtime is player specific.
4) days count.
5) Realistically I am really looking at day tracking more than week tracking, skills are day based. Mostly this is for training anyway. I see acquiring gear as setting a delivery date that locks out downtime for training (&CfK), so even uptime would not stop the clock ticking for that.
5-4) Their will be no choice at the players end for downtime length, so no player can hold up a player. At the start of downtime I will declare its length, this is then out of game time, a montage until the inevitable "two weeks later".
6) still looking into this one, off the top of my head the trainer would be like a device rating, all dice rateings equal that, min 3. As you saw I am concerned about traininers over rating 6, they should be npcs or contacts.
7) "in", autocorrect... Assumption is correct, your not likely to see 3 weeks though. Just re-inforcing this when I can.
8 ) Contacts sourcing takes up the contacts time not yours - will explicitly state that.
9) likely to be expanded somewhat, each contact will get a "uses" list like in the main book, "gear" will state type, and a broadness. The three catagories of broadness are roughly.
Unrestricted: eg a fixer, can get anything, but uses base connections.
Focused: eg a corporate Johnson or milspec gear smuggler, can get items related to an area or theme, can be restrictive, connections +1.
Specific: can get gear only in a very narrow area, eg talismounger, vehicle parts, medical supplies, guns. Connections +2.
Still contemplating this, has been my main delay.
10)

Read the FAQ, the sentance I wrote is just a reminder of the last paragraph. Will just post it into the forum actually, easier.
11) This is GM call not missions. Mostly due to the shock caused by the downtime restriction on sourcing gear. Something I am happy to allow, the use of edge before the session

. The other bonus is its an actual roll if done in game, not buying hits. Anyway, similar to binding yes. The initial test takes hours. Realistically if this would occur in the prep day time before the run that I take out of spare days. If successfull, the delivery time is set, as said earlier the delivery time can overlap with both uptime and downtime, just locking out any other downtime activity until finished. Will flesh this out more, text was brief.
12) I'm also looking at putting a cost on acquiring contacts in game, to stop them getting prolific. Basically the 1 karma a point thing from character Gen, but allowing cash to be used in proxy, at CfK rates. Still thinking on it... also adding a rating 0 loyalty, "hey don't I know you?" For contact you want to purchase but have not cemented a rating, they won't do anything for you, just you have them on the books.