I would definitely recommend your wife progressing through the MSQ with regards to her main job. She can use PotD to get pugilist to level 15 (so that she can unlock bard), any alternative classes/jobs she would like to level (I would recommend getting Lancer to 34 for Blood for Blood, but that is entirely optional for the time being), and during any lulls there may be in MSQ quests. I know that there's a little bit of a lull around level 44-ish, but you also have two dungeons you can do during that time to try and give you a little bit of experience (especially do them for the first time bonus experience): Dzemael Darkhold and Aurum Vale.
Dzemael Darkhold (Level 44 dungeon)
Aurum Vale (Level 47 dungeon)
Both of these dungeons are unlocked via Sidequests, so your wife will have to step off to the side from the MSQ for a bit to unlock and run them. I, personally, don't find either that bad, if you can get a good group for them. And both give nice amounts of experience. I also recommend her keeping up with her Hunting Log, as that's basically free and easy experience, and completing her Guildhests up until the final one at level 40 for the first time bonus experience as well. Do Leveling Roulette daily, since it also gives a very nice chunk of experience regardless of the duty you get.
Obviously, with any other lulls in levels between MSQ quests, your wife can fill with PotD or, even better, Daily Roulettes. Once she hits Heavensward, I don't remember there being any significant periods where you have to level up to progress with the MSQ; maybe around level 55-56, but she can easily get plenty of experience by running her Daily Roulettes (be sure to have her unlock as many level 50 dungeons as possible so she can do her Level 50 Roulette--some level 50 dungeons are Sidequests, and not part of the 2.x MSQ, so she'll have to do a little bit of digging, but the FFXIV Wiki and Gamer Escape sites has pages for each dungeon, and the quests you need to unlock them).
Obviously, if she has additional questions, feel free to ask them here. A lot of us are more than willing to help out fellow players, especially those that are returning to the game. :3