Firstly, is it 90 days after or 90 days from the entry date?
Not sure what you mean. Do you mean whether it is December 6 or December 7? I believe the day of entry counts as a whole day, so you should assume you will be admitted until December 6 (meaning you can stay until the end of December 6).
Secondly, does my 3.5 week trip to Mexico reset my clock? Well, I
understand that travel to Mexico shouldn't, but my understanding is
that CBP can award a fresh 90-day window on re-entry should it be
clear that I am not trying to game the system.
Since you will be returning before December 6, CBP has the choice of either re-admitting you for the remainder of your initial period of admission (i.e. until December 6), or considering you for an entire new VWP admission of 90 days if you tell them of a need to stay longer than December 6. If they are re-admitting you for the remainder of the period, you do not have to be returning to the US on a VWP signatory carrier. If they are considering you for a new VWP admission, you have to be returning to the US on a VWP signatory carrier.
See 8 CFR 217.3(b):
(b) Readmission after departure to contiguous territory or adjacent
island. An alien admitted to the United States under this part may be
readmitted to the United States after a departure to foreign
contiguous territory or adjacent island for the balance of his or her
original Visa Waiver Program admission period if he or she is
otherwise admissible and meets all the conditions of this part with
the exception of arrival on a signatory carrier.
And 9 FAM 201.1-4(C).e(2):
(2) (U) Side Trips Permitted Within 90-day Limit:
(a) (U) Travelers participating in the VWP who make their initial
entry into the United States by air or sea must arrive aboard one of
the participating carriers. After the initial admission into the
United States, under the provisions of VWP, a foreign national may
temporarily depart to, and return from, Canada, Mexico, or adjacent
islands by car or other carriers if the total stay in the United
States and the time accrued in contiguous territory and/or adjacent
islands does not exceed 90 days.
(b) (U) In other words, a side trip to Canada, Mexico, or the
adjacent islands does not “reset the clock” for VWP travelers, unless
the traveler is resident in the country to which they travel. (For
further information see Chapter 15.7(i) of DHS Inspectors Field
Manual, Readmission After Departure to Contiguous Territory or
Adjacent Islands.)
(c) (U) Return from Canada, Mexico, or adjacent islands by air or sea
within the 90 days limit does not require transportation by a VWP
signatory carrier.
And chapter 15.7(i) of the CBP Inspector's Field Manual (There are various copies of it on the Internet, e.g. here or here. The IFM has reportedly been replaced by different manuals at the CBP, but there isn't a more updated comprehensive manual available online):
(i) Readmission after Departure to Contiguous Territory or Adjacent
Islands.
(1) General. Aliens admitted under the VWP may be readmitted to the
U.S. after a departure to foreign contiguous territory or adjacent
islands for the balance of their original admission period, provided
they are otherwise admissible and meet all the conditions of the VWP,
with the exception of arrival on a signatory carrier, in accordance
with 8 CFR 217.3(b). The inspecting officers also have the discretion
to grant the applicants entirely new periods of admission, providing
they are arriving on signatory carriers. The following sections
discuss the criteria, procedures, liability ramifications for the
carriers, and define the term “adjacent islands” for the purposes of
the VWP.
(2) Conditions for Readmission. As discussed above, aliens admitted
under the VWP may be readmitted to the U.S. under the VWP after a
departure to foreign contiguous territory or adjacent islands provided
that:
- their authorized period of admission has not expired,
- they plan to depart the U.S. prior to the expiration date of their period of admission,
- they present valid, unexpired passports which reflect admission to the U.S. under the VWP, and
- they continue to meet all criteria set forth in 8 CFR 217 and section 217 of the Act, with the exception of arrival on a signatory
carrier.
If the alien still has the original endorsed departure portion of the
Form I-94W, admit the alien for the balance of his/her original
admission period. [...]
If the alien needs to stay in the U.S. for longer than the original
period of admission, the officer can consider granting another 90-day
period of admission, provided the alien meets the requisite criteria.
These cases are considered new admissions and the officers should
follow the applicable procedures provided in Chapter 15.7(c), Air and
Sea POE Arrivals, or Chapter 15.7(d), Land Border POE Arrivals.
Officers should be aware of the potential for fraud in certain cases
of repeated entries, although legitimate cases should be given due
consideration.
If the original period of admission has already expired, the alien
cannot be considered for readmission and must meet all the
requirements for a new admission into the U.S.
Your last question:
Additionally, is there a way to check when CBP marked me as having
entered the country (and thereby started the 90-day timer) or exited
the country (and thereby stopped/reset the 90-day timer)?
On the CBP's I-94 website, you can look up your current I-94 and travel history (the dates when you entered and exited), although I am not sure what you mean by "marked", because it should be the same as the dates you actually entered and left.