Arborists aren't trained for this kind of work so you are on your own but you can probably find some kind of video about maintaining espaliers, which require a different strategy than free standing trees- for one thing, it is standard to do almost all maintenance pruning during the summer. Of course, such a video won't guide you out of your current pickle. Corrective pruning is a subject that doesn't get much coverage, even on the internet and yours is a very specific case. I should make a video of making a hinge to bend a branch but don't have the equipment. The important thing is not to cut (much) more than a third of the diameter and do it on the side your are bending it. Use as many cuts as it takes to make the branch reasonably limber working your way up the branch. The suggestion of taking it out of espalier form and turning into a conventional free standing tree is also a workable strategy and good idea, but the question is, would this work within the space? Espaliers are attractive but somewhat complicated to maintain as productive trees. But then, that can be said for all corrective fruit tree pruning. Apple trees are relatively forgiving of transplantation. Here is a publication that begins to explain some of the biological issues you are dealing with. If you are interested, I can find you more. Here is a link that might be useful: fruit tree physiology

Dave, you might not like the answer I offer, but I'd leave it be. KCT is notoriously ungainly in youth and especially in non-leafed-out condition. Despite those factors, it usually shapes up just fine on its own. Not a tree with an especially pronounced central leader-it's cool that you know about the importance of that in many species BTW-it will still do its thing and usually be fine. The tree is too young to worry about, IMHO. +oM

Cool your willing to use a make shift gritty mix. May want to sift some of the peat materail from the BBS bagged C&S soil as well. What remains after sifting is some darker bark pieces that looks like a finer mulch and some forest humus. Useable yield may vary, would think one bag of BBS unsifted bag O'crap should yield enough for all of them. You could also ( with some extra time on your hands) pick up a bag of orchid bark smaller size is better but any size will work from a BBS as well . After soaking them in warm water for a while the chunks will be eaiser to ( by hand) break it into smaller barkier pieces. Prior to sifting any especialy for Perlite I'd suggest to use some sort of mask for beathing protecing. Big drainage hole ? As in orchid pot drainage hole big ? The demo pic is a bit off. less humor or more fun ? Blue arrows. look sort of good as ASAP potting candidates for some practice for you but if me I'd cut them for newer cleaner root. Red lines suggest cutting them for re rooting and potted later Purple circle I'm Sort of mixed on this one. It can go either way. Bigger can survive longer but adapts more slowly.

Your very young tree needs as much foliage as it can grow at this point. I would not prune anything for at least another year or two. Citrus are not like other fruit trees like peaches or apples that need to be trained young. When citrus trees are young they they should just be allowed to grow freely, and put on lots of foliage. Citrus trees can be pruned for shape when they are older with no problems. But your tree is so young and has so little foliage at this point that it needs all it's leaves. More leaves means more roots, which will grow more leaves, which will make more roots, that will grow more leaves, and so on. It also looks to be a seed grown tree as many Kaffir trees are, so they are not suckers. So in short, don't prune anything now. Don't prune anything next year either.