@Everyone
I plan on a month passing in game between Adventure 1 and 2.
@Chrome
Training Intimidation to 1 takes 1 day, doubled for the dependents to 2.
Increase Edge to 2 takes no time
Extra secure in the Warrens means you are paying the 20% lifestyle increase to a local gang - which one will vary depending on whether you want to live near Jack, Hubert, or Amy's current location.
As far as classes for Sam, nothing really outlined in this in any sourcebook, so we will be playing it by ear. No SIN is a big problem. You can't get anything legal, and I can't imagine anyone running any quality education programs for the SINless due to lack of funds. Realistically if you want to get her something good, probably better for her if you get a fake SIN for her - rating 2 would probably suffice. Since you are already getting a rating 4 SIN for yourself, and that 5,000 may be too steep, you can probably get a glorified babysitting service in the meantime.
Reagents: You had 10 Shamanic and 100 Hermetic before the apartment and interrogation. you used 21 reagents between those two scenes. Assume that you used the last 10 Shamanic, and then 22 Hermetic. That leaves you with 78 Hermetic Reagents left. Hubert will exchange those for 58 Shamanic Reagents.
As far as purchasing new Reagents, they are 20 nuyen plus the markup - there isn't a bulk discount. Remember that even a good harvester - Magic 6, Alchemy 6, gets about 2 drams per hour of searching (assuming he is in the right environment) - and that hour exhausts that hectare for 2 days. Hubert certainly doesn't have hundreds on hand, he is busy keeping his community whole with power, food, and medicine, and doesn't have time to devote hundreds of hours to acquire the reagents you need.
You can certainly negotiate, but without the skill, your odds of success against any talismonger are fairly slim.
For the focus, Hubert can identify it for you, it is a Ritual Spellcasting Focus, Rating 1 - so street value of 6600, so the base value of what you could fence that for would be 1650

+/- hits on any negotiation test.
Glad you mentioned the gift to Hubert - it should be substantial, in addition to the in character background help he provided, in game you will have asked him to:
1) Provide childcare for Sam and Kevin
2) Identify the focus (if you look at page 389 you'll see that he does this for you under the table, but would still charge you what the market would bear for this service)
3) Exchange Hermetic for Shamanic reagents at an unfavorable rate (for him)
None of these justify the listed cost of Loyalty x 1,000 nuyen (all 3 would not be 5,000 let alone 5,000 apiece), but the gift should probably be closer to 1,000 rather than 100 if you know what I mean. Lots of options for you - another generator, equipment for the children, tools, clothing, basically anything necessary for a small community (and cold hard cash doesn't hurt either).
As for the Availability tests for Chapel, here they are, in order the SIN and then the License
14d6.hits(5)=2, 14d6.hits(5)=8And their rolls
12d6.hits(5)=5, 12d6.hits(5)=3So the license is available in a short period of time, he'll need to try again for the SIN
Chapel
14d6.hits(5)=5Gear
12d6.hits(5)=2So about 4 days for the SIN
So your costs, as far as I can tell are:
Fake Sin Rating 4: 10,000
Fake license for Magic, Rating 4: 800
Squatter Lifestyle, Dangerous Area: 400
Low Lifestyle, Dependents, Extra Secure, Dangerous Area: 2,600
Trodes: 91 (assuming you are still buying them)
Gift to Hubert: putting in 1,000 as a place holder for now
Leaves you with: 10,729
This doesn't include selling the Focus, or buying reagents obviously.
@Jack,
You mentioned getting something for Nic, this would definitely be appropriate given the babysitting he provided (as well as crash space) for the team.
@Grease,
Are you going to attempt to resist the Novacoke bender, or are you voluntarily going to get high at the end of the adventure?