I think a lot about training apple trees because it's part of my living. I also get lots of opportunity to see the consequences of bad decisions early in a trees development a few years down the road- often my own bad decisions. What you do to develop a productive framework of scaffolds depends a lot on the variety of the tree and its rootstock. If your tree is a vigorous grower like Fuji or Granny Smith those 2 scaffold branches may be more trouble than they're worth. In such varieties a scaffold branch more than a third the diameter of the trunk at the branches point of attachment may grow with excessive vigor, delaying the trees fruitfulness and throwing your plans of a Christmas tree shaped central leader out of whack as those branches dominate. In spurry, early bearing varieties like Goldrush or Ark Black such "oversized" scaffolds will probably not be a problem because the diameter won't cause excessive vegetative vigor because the early fruiting will calm vegetative growth. If the rootstock is M26 or anything down in vigor managing vigor by removing excessviely large scaffolds may not be important. I have an article that I've written about the training of fruit trees using ratios as a guide. E-mail me if you'd like a copy.

The two of you have performed a limited experiment where your site was the control. Of course your soil may be different as may be water management but it's interesting that he got much more vigorous growth. New apples are usually transplanted 2-year trees that suffer root damage when being dug up and therefore don't tend to respond the first season to fertilizer applications although they may grow faster the second season as a result of applications the first. The only consistent advice I read about fertilizing these trees is don't put quick release fertilizers in the planting hole. I wouldn't describe a rapidly growing new tree as "running amuck" unless maybe it was my neighbors tree and was planted at the same time as my runted one. Then I'd probably do exactly as the neighbor did to try to duplicate those results. If it runs amuck then you should pinch prune it to get it running right. Anyway, I suggest the MG if that's the fertilizer of choice, although any quick release nitrogen would likely have the same affect at same rates.

Passiflora/Passionflower. Probably maypop if it's wild.

"Is this the reason for the apparent slow growth?" We can't tell why your tree is growing slowly from the information provided. My first shot-in-the-dark guess would be that it might be grafted onto a dwarfing rootstock. Roots coming from the scion would NOT make growth slow. If anything it would increase growth rate. "If I clip those roots off and remove a little dirt to lower the soil level will that reverse this?" No, it will not increase growth rate. However, I would definitely recommend removing the grass clippings from around the trunk. A situation like that will often lead greatly increase the chances for disease, rot, and even pests problems. If you decide to allow the scion to continue producing roots (and therefore killing off the rootstock), you might cover the existing roots with a light layer of soil. However, I would definitely not keep piling grass clippings up against the trunk. Also, be aware that if the scion roots and the rootstock is killed off, your tree could possible suffer in various ways (introduction of rot, poor root anchorage, etc). You might find more details about this with a search of this site. There are at least a couple of threads about scion rooting/root-stock ellimination. "Or, just how do I handle this and help these trees grow better?" Do you know what rootstock the tree is grafted onto? Did you plant the tree? Can you give us more details about how it was planted? Are there any signs of problems besides slow growth? Have you had your soil tested for nutrient levels? There are just too many variable to know what's causing the slow growth without more info.