Drill baby, drill!
For the 2 switches under the 'shift' keys, I lined the top/bottom and left/right grids of the switches above and to the side and carried those lines into the empty area for the new switch. That gave me a near perfectly positioned square for the new switches. I approximated near center and slowly drilled a hole big enough to insert a file. A set of small files with various profiles cost $5-$15 at hardware stores. Harbor Freight has them for about $5 what costs $16 at Home Depot for a package of about 6-7 files. Some other hardware/hobby stores sell them individually as well. I use a combination of flat files and square files. Very easy, and I'm a detail nit-pick for this type of thing. If the hole is too small, the switch gets squeezed and won't operate well. If the hole is too big, well, you screwed the pooch. As you get close, just keep test fitting till it's right. You can use a little hot glue just like Kinesis does to lock in the switch. You will want to note where the switch corner pops out on the back side, it may need to touch the pcb on the keywell and you'll have some fiddling to get it in correctly. Really no big deal though. And the angle of the switch will be fine in the mounting in the keywell, No other mod needed.
For the F-key plates I had to do some serious measure and mark, insert and evaluate. several times to get the positioning correct. These are not absolute. I needed to cut the case holes FIRST to do this. You have a couple decisions as far as exactly where the switches are positioned. Obviously, I wanted them as "in-line" with the matrix as possible. You also can decide to slightly angle the plate when you put it back in (toward you/away from you). Then using the same spacing as between cherry switches, mark the lines that result in squares (it will look like grid paper) and drill a hole in the middle and file.. Use hot glue to lock in the switch. This will be tedious if you have metal plates, if you have the plastic/fiberglass, it goes much quicker. If for some reason you make a massive mistake, the piece can be replicated from almost anything (unlike the keywell). Regardless, this won't get done in one evening.
I have had NO regrets, and NO 'I should have left it alone' thoughts. I seemed the thing to do before I did it, as I was doing it, and after I did it. It's the way the keyboard should come, no doubt about it. I have not done it to my one-piece Kinesis yet, but I will when I finish deciding on the volume/multi-function knob mod, then do them at the same time. This summer is an exciting time for my Kinesis projects. I am confident you will be thrilled and ask yourself "Why didn't they do this???". I'd say the quality of my modding/adding of the switches came out about 99%, and that's good in my book.
In a day or so I can take some things out and take some better pics that might be better illustrations for you, if you like.
As far as the other keys in the thumb area...depending where you want them, there are some potentially challenging considerations due to the existing pcb locations. Decide on key locations first, then worry about how to make it work. Can you post a pic with the exact key locations marked with tape or photo editing?