I use a weird mix, depending on situations and character. I installed
BindPad which has allowed me to put utility items into keybinds that make sense to me (things like the down arrow for my smart mount macro, shift+down for hearth, control+down for my engineering wormhole, alt+down for the crusaders' tabard, etc). I also use it and
Clique for a mixture of things on my holy paladin, so like middle mouse button to cast Flash of Light and shift+middle to cast holy light (thanks to clique), but a macro to cast divine plea but pop wings/trinket/divine illumination/etc with alt+middle bound in BindPad. For this whole thing, I keyboard turn (wasd movement keys) but have control as my vent key, so am used to using my pinky to hit keys.
Also, most people that I've seen with lots of keybinds do it the same way I do, the modifier keys (shift, control, alt) with a mixture of a key on the keyboard. Also, don't overlook any mouse buttons you may have and the fact that you can also add in the modifier buttons to those mouse buttons as well as combining modifiers (control+alt+key type deals). In my example above with the down arrow key? I have smart mount, hearth, tabard, engineering wormhole, 100% land mount, 60% land mount all bound to that one key, with combinations of the modifier keys. For the directional keys in general, 4 keys total, but 10 different things I can do (eat/drink/swap specs, including a special one for going pvp, as well as those 6 others listed).
If you want to experiment more with keybinds, I found BindPad to be the easiest way for me to do it, since Blizzard's menu is horrible (seriously, if you look at that, how do you know which bar on your screen corresponds to action bar 8? Especially if you don't use any sort of action bar mod?). I'd also recommend doing utility spells first, things like mounts/portals/pets/professions, as something to get used to hitting keys rather than buttons, but nothing that would impact gameplay (DPS/tanking/healing).
Also, figuring out which spells you need when are helpful, and maybe the issue isn't keybinds but the layout of the action bars. Paladins have all their helpful "hand of" spells that are pretty much only ever going to be used rarely and in a party, same with divine intervention. Setting those on a bar that is then set to only show when in a party (and could be further refined to only be visible in combat), will also help reduce any feeling of actually needing to click things.
Also, for the spells you use the most, why have them on the number keys if they aren't comfortable to use? With being a keyboard turner, would having frequent spells on cfr be more comfortable? What about using the numpad on the right-side of the keyboard (or even use that to keybind the various raid charms and remove any addons related to those)?
The whole thing is what is comfortable for you, in regards to how flexible your hands are while playing, as well as how your keyboard works with your playstyle.
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