I'm so glad Kiwi is in the home-stretch of this illness, I love happy endings!
As far as toweling goes, I too absolutely HATE having to do it to any of my guys, and I avoid it whenever possible, but it is necessary and can't be avoided at times. If that's the only way you can get him to take his meds then that's what ya gotta do...But it does not automatically mean that it will cause an issue with Kiwi and yourself, not by any means at all.
A lot of great tips have already been given, the best being "Let the towel be the bad guy, not you" by allowing Kiwi to attack the towel first, and then doing what you have to do, and afterwards allowing him to again attack the towel and find his own way out of the towel, with you already having walked away from the situation.
My Senegal, Kane, particularly hates the towel, and of course he's the largest bird I have and the one with the beak that can really do some damage if he wants to. He thankfully allows me to clip his toenails without the towel (thank you to his breeder!), but when he was only about 10 months old he got his backwards-facing toe on his left foot stuck in his cage bars where they join, and he chewed-off about half of his own toe to fee himself (I wasn't home at the time, and that cage is no longer with us)...By the time I got home he was still stuck in the damn cage, even after chewing off a good portion of his entire toe, and he was screaming in agony and fear. I immediately (and instinctively I guess, not really thinking in the moment) just grabbed him and was trying to figure out how to free the "stub" that was left with the half of his toe hanging on from a thread of skin/bone, because he had already bled what looked like his entire blood volume all over the floor and the cage bottom. I thought he was going to die, so I just grabbed him and it took me between 1-2 minutes to figure out that to free him I had to actually "slide" his foot upwards, as this must be how he got stuck in the first place, he was standing on the curved part of the dome-top and he "slid" down one of the bars and right into the joint where the front, top, and side panels joined. So to free him I had to slide him back up...Well in the 1-2 minutes it took for me to figure this out, Kane had literally sunken down onto my right thumb and never let go. When I finally freed him I set him down on the kitchen counter and wanted to run to get a towel and the cornstarch, but he still wouldn't let go. I thought I was going to lose my thumb too, lol, we'd both have "nubbins"...he finally let go, I ran to my pet first-aid kit and grabbed the corn starch and a towel from my linen closet, and when I went to towel him he simply climbed right onto my chest and buried his head...poor guy was exhausted...So I just wrapped him up and into the car we went, with him screaming from inside the towel (he's flighted and I was just carrying him outside, not good but he was bleeding to death)...My CAV removed the remaining toe that was hanging, made a skin flap, and stitched it shut, all while I was holding him inside of the towel, with his little face poking out looking at me, and I was certain that he was going to hate me forever for this...HE WAS WATCHING ME, LOOKING AT MY FACE THROUGH THE TOWEL THE ENTIRE TIME, NO ONE ELSE, IT WAS ALL ME, ALL MY FAULT! My CAV did a wonderful job, you can't even tell he's got a "nub" or a "stub" unless you are looking for it, but he was not pleased with me for a day or two, though he did spend the rest of that night after we got home from the vet sleeping on my chest, so he wasn't that angry...
My point is that you have to do what necessary for your bird's own good, and even though it might upset him at the time, it will not at all, in any way ruin your bond with Kiwi. He'll be fine, remember, "It's the towel's fault!"