After trying barrie, trubalance, and hampton, I've found modified is the best fitting alden last for the narrow heel/flat arched foot, providing you can deal with the higher arch. I haven't had much luck in the 1,5, or 7 lasts from AE. 5 last seems to be the closest fit out of those.
3/4 insoles with arch support help support the arch, which will help bring it up to normal instep height. Tongue pads help quite a bit too. I've tried quite a few 3/4 insoles, and prefer powerstep and superfeet (the full length black with the toes trimmed off). I'm going to try the birkenstock insole soon, lots of people seem to recommend that as well.
I think flat feet/pronation generally tend to cause the pinky toe to splay out, which can also be problematic. Wood shoe stretchers with the bunion attachment can help widen the toe box. The only stretcher that seems to fit in a dress/work boot is made out of aluminum and quite costly. It might be better to take boots to the cobbler for toe box stretching. That said, they only go so far. I've learned how to make the go/no go call on pinky toe tightness with some experience.