I would:
1) Probably not build a box over your HVAC unit. Seem like a lot of things could go wrong there, for minimal benefit. I might consider gluing rigid foam on some of the sheet metal panels, or just laying a piece of unfazed batt over the top of a horizontal unit. Beyond that and you're experimenting with outcome factors like fire, carbon monoxide, and condensation.
2) See if I could slide a couple inches of rigid foam under the drip tray where you can't blow in insulation or add batts. Good news, the flex duct won't stop you!
3) Ductwork is hard and expensive to insulate to any reasonable amount. Here's an easier way for long stretches. (1) Screw stakes to the ceiling joists along both sides of the ducts, so they stick up in the air. (2) Staple landscaping fabric (which is cheap) to the stakes, creating a little fence that goes alongside your ducts. (3) Blow cellulose into the cavity created by the two fences alongside your duct, burying the duct under a foot or so of cellulose on all sides. Note that this uses a LOT of cellulose, but cellulose is cheap. For the short stretches, or where the duct goes through the ceiling, Just drape a big batt over them and dust over them with cellulose.
4) If high attic temps in the summer are a concern, radiant barriers on the rafters are cheap and easy. Also, 100 year old houses rarely had enough ventilation, so add a whirly vent, a ridge vent, and/or some intakes in the porch ceiling. When you replace the roof someday, go with a light color.
5) The #1 efficiency killers for forced air systems are grossly undersized intakes. If you have this problem, fixing it will save more energy than a lot of the insulating ideas.
6) The #2 efficiency killer is dirty inside and outside coils that have never been cleaned.