Learn English – Comma before and after “and” and again after non-essential information

It looks to me like you've already answered your own question. "It should be done consistently." Follow one consistent pattern within the narrative. If you (by which I mean your wife) want(s) to insert extra commas in the dialog to show pauses, that's your prerogative, but make sure that there's actually a reason for the pause caused by each additional comma. If it doesn't give any additional meaning, remove it.

The prescriptivistic and potentially outdated grammar of Elements of Style lists a rule (in Chapter 1, part 4) for placing a comma "before a conjunction introducing a co-ordinate clause" (unless the conjunction is and or but and both clauses have the same subject). That could work as a reasonable ground rule for where to insert commas in the narrative, but it can be customized as you see fit. It's a novel, not a piece of academic writing, so it's up to you to decide on your own rules for when commas are needed.

There are plenty of acclaimed modern authors who use almost no commas at all. The general modern approach to commas is the fewer the better. If you can't think of a specific reason why a sentence needs to have a comma, it's better to leave it off.

Your use of commas is fine in the five numbered examples you presented, and your career counselor offered you confusing advice about punctuation (even though she may be outstanding at career counseling in general).

In terms of substance, excellent computer skills involve a lot more than typing speed, which is a relatively small part of computer literacy. Far more important is your familiarity with Microsoft Office programs, including Word and Excel, and especially any proprietary or specialized software specific to the industry in which you seek employment.

Speaking strictly for myself, as an employer I am put off by an applicant who thinks it is important to mention his or her typing speed in a cover letter. There are exceptions, of course. If it has been your life-long dream to become a medical transcriptionist, for instance, then it would be very important to highlight that ability, along with an outstanding medical vocabulary, excellent editing skills, and exceptionally good comprehension of spoken English. Otherwise, it just sounds like you are bragging. Please keep in mind that the person who reviews your application probably types at 40 wpm or less. As a Stanford graduate, you hopefully will not spend eight or more hours a day speed-keyboarding, which is extremely tedious and stressful work.

If you want to keep it in, then I would recommend, "I have excellent computer skills and a typing speed of 80 WPM. I'm fluent in [...] Microsoft Word and Excel, as well as [...] Adobe Photoshop and other imaging software" (or CAD/CAM applications, GIS software, or other specialized programs in math, physics, design, layout or whatever else may be required for the job). Under no circumstances should you write, "and therefore I deserve..." anything! An entire generation of students raised with the fantasy that everyone should have high self-esteem (rather than "accurate self-knowledge") has created a false sense of entitlement that clashes with the reality of working in the real world.

The key is always to write for your reader, not for yourself. Put yourself in the employer's position, and ask yourself what you would want a highly qualified applicant to say about herself in her cover letter. Try to avoid cliches and be honest and direct about your experience, education and accomplishments. You'll find that it results in far more positive responses from your prospective employers.

Good luck, and don't worry about your use of commas. You've got it!