You will learn patience pretty quickly, I think. Join a group buy or two.. try to hunt down that exotic keyboard part.. wait for shipping from far-off lands.. try to win Clacks and Bros.. I think after you do some of that stuff, you will be a much more patient person; I know I am, anyway. It's all a part of the fun of this hobby though! 
Feels like victory when you finally acquire that hard to find item after a month or two of searching.
)
I definitely recommend one of Bpiphany's custom controllers, they're great. Programmability is a really powerful thing to have on a keyboard! Custom FN layers, key reassignments, macros, mouse keys, etc.
They don't require any soldering either, you just open the case, pull out the old controller and drop in the new one. He makes one for the full-size Filco MJ2, I believe it's the Kitten Paw?
I know full-size vs. TKL is a personal thing, but have you considered a TKL board? The ergonomics are much more comfortable, IMO.
I think I'll start off with a 104, and venture into TKL's later. I use my numberpad a lot.
I'm super intrigued about the custom controller. How does the software work? (I'm comfortable with soldering & light programming.) Is it mapped in code and then flashed to the controller? I couldn't find any info about that specifically reading through the link you gave.
I use this for my Frosty Flake, Phantom, and JD40, it also works with other boards as well:
https://geekhack.org/index.php?topic=51252.0Super easy to use, and pretty powerful. The only kinda tricky bit about programming the board is the first time you program it, you need to run a somewhat strong magnet (a normal fridge magnet didn't work for me) over the controller to trigger a reed switch to put it into bootloader mode. You can then use Atmel Flip to load your hex onto the controller. You should only need to use the magnet once, as you can program a key combination to put the controller into bootloader mode afterwards.
TMK probably also works (I can't confirm because I haven't looked into it for this controller, but TMK seems to work for most boards).
TMK:
https://geekhack.org/index.php?topic=41989.0If you're comfortable with coding, TMK could be perfect for you. I still haven't gotten around to learning how to use it (soon

), but I know it's quite advanced. A lot of cool features in TMK.
So far, I only have experience with Easy AVR and Soarers.
I also use the numberpad now and then. I have a Filco separate numpad I use, but most of the time I use an embedded numpad that I have programmed on an FN layer on all of my boards. If you use it quite a bit though, I can see how it would be more convenient to have a dedicated numpad.