Okay, so the first tranche vests after one year (5,000 options), and the rest vest monthly over the remaining 36 months. (I'm assuming the 1/48th is a typo since that math doesn't work for a 4 year vesting term. Otherwise, if it's 1/48th and 1/4 after year one, that's a five year total term.) Just because they vest doesn't mean you have to exercise them. For purposes of talking about the holding period below, though, I've assumed you will immediately exercise (although you don't have to and may not want to).
Grant Date: December 2011
Vesting Commencement Date: October 2011
October 2012: 5,000 vest and become exercisable
November 2012: 416.67 vest and become exercisable (assuming there's probably a provision in there rounding it up to a whole share, with the very last month making up for the difference, so 417 each month until the last month)
December 2012: 417 vest and become exercisable
etc.
Holding Period: To get capital gains treatment, the stock acquired by exercising the option must be held until the later of: (i) One year following the day the stock was transferred to you on exercise; and (ii) Two years after the date the option was granted to you.
Later of: (i) If you exercise immediately after vesting, for the 5,000 this would be October 2012; or (ii) January 2014 (depending on the exact date in December they were granted. I'm being cautious here). This means for the first tranche to get the best tax treatment, you may not sell the underlying stock (once exercised) before January 2014. If you wait, all of the gain will be capital gain. If you sell before the holding period, the spread will be ordinary income (the different between the FMV at the date of grant and the price at exercise) and any subsequent appreciation will be capital gain.
You have to do this calculation for each tranche as it vests and you exercise.
Does this make sense?
The second provision you quoted is boilerplate. The Internal Revenue Code only allows up to $100,000 to be awarded as ISOs (because of the favorable tax treatment) before they force any other options to be treated as nonqualified. I think it's $100k per year, but I'd have to confirm that. I'm assuming the Notice of Grant designated them as ISOs.
Also, take a look around the award agreement and/or the plan document and see if it accelerates vesting on a change in control. Sometimes they do, sometimes they don't. That being said, if vesting is accelerated on a CIC, then all of the outstanding options would vest at that time and that would affect your holding period calculations if you exercise immediately after vesting.