Haha, you get used to it.
Got a friend that uses shift j to sheep… he’s a multi r1 mage he’s also super skinny 
Beside WSAD, 1,2,3,4, mouse buttons, I also use Q,E,R,F, Z,X,C in combination with CTRL, ALT, SHIFT modifiers. Except I don’t need modifier on them all.
So, yes, I use shift, ctrl and alt.
I move with WAD so I find it super smooth to use S for my main attacks.
Things I want to be really fast with goes to the mouse such as trinkets, cc and kick. I mean how easymode isn’t it to just scroll up for an important spell as kick.
Offensive and defensive cooldowns I need to be fast with goes to keybinds close to my movement binds.
Not a big fan to streach my fingers to §, 1,2,3,4 and 5 so I only use them for binds I don’t need to be fast with.
I even found V more comfortable than those.
Oh your problem is very easy to solve by becoming left-handed 
Every key turns into 5 - clean, shift, alt, ctrl, shift+ctrl all with just your thumb.
I use an old Belkin N52te, which has 14 normal keys, a thumb stick and two more buttons under the thumb. It also has a wheel but I find that a bit awkward to use.
I also use a Roccat Nyth mouse, which you can choose the button layout on. You can have up to 12 thumb buttons but I only have 6 set up.
I use a combination of mouse and thumb stick for moving and looking around as I move.
I have shift and CTRL modifiers on my mouse. Which puts 42 keys in easy reach right under my left hand. I also have map and jump buttons on my mouse, plus some other stuff. One of the thumb buttons on my keypad is the ESC key. The other is a macro’d panic button (Vanish, Cloak of Shadows and Sprint). There is another modifier key on the mouse that changes all the thumb buttons, too.
I have yet to find myself short of easy to reach keys.
1,2,3,4,5,6
Shift+1,2,3,4,5,6
Q,E,R,F
Shift+Q,E,R,F
and more mouse buttons
` to 6
Alt + ` to 3 (and Q)
Q E R T Y
ctrl + 2 to 4
F1 to F5
And my mousewheel-click is something like ghost wolf, divine steed, shapeshifting 
Edit: had to put it in code because the char before the 1 is breaking it.
30+ years of muscle memory helps a lot. If it ever used to cause me discomfort, it doesn’t now. I also played the organ and guitar before heavily starting to use a computer keyboard so was used to stretching my fingers.
How exactly is reaching for these keys hurting your pinky? Is it because you have to stretch too far, or contort your finger/hand in a weird way? Have you thought about rebinding your movement keys to something like ESDF? It should open up a few more keys for you to reach even if you still can’t press Ctrl and Shift comfortably.
I cleared up q, e, r, t, f, g, z, x, c, v, b and s. Made q and e become a and d and moved the rest to the other side of the keybord. I use those and 1 2 3 4 primarily and I have things that I can take more time on doing at 5 6 7 8. This works for me. Takes time to get fully used to the new type of movement but you have so many buttons in quick to reach places.
Oh yeah I also use two buttons on my mouse
The reason it hurts to reach these is because my finger is bent back on its self so much to reach Ctrl im pushing down on the key with my finger nail and not my finger tip, if that makes sense, so after a week of trying to get used to Ctrl my pinky finger nail has a stabbing feeling every-time i press down on it now :S
Thats why i wondered how other people do it, unless my hand are just weird lol.
I dont care what spell or rotation will be easier if I bind a spell to 6, it will never happen 6 is always my interrupt !
I used to use an MMORPG mouse. I played a game where I had 12 buttons, and with alt and ctrl I turned that into 36, and then there were the back/forward buttons on the mouse to which I did the same… That time has passed though. I have 6 extra mouse buttons on my mouse and I use exactly 0 of them (G602), the buttons are extremely uncomfortable to use (big mistake in mouse). On my mouse I do use the back and forward buttons.
The 4 skills to the right are the back/forward + alt variations. M3 is the middle mouse button click and N9 is capslock rebound: https://imgur.com/a/v2TxBc0
Generally speaking I try to keep skills similar based on what they do (though not always possible), and I try to keep skills at the same binds between specs. My keybinds are designed around being easy to reach and avoiding crampy fingers. My hands and fingers get sore really quickly, up to a point where I get sharp pains in my fingers or nagging feeling in my lower arms, so I work my keybinds around that. My movement is all based on QWASDE and I frequently hold my RMB to optimize mobility and strafing. I kept my scrollwheel for zooming, as this is frequently needed.
General setup:
-
<1>is a resource builder -
<2>is a resource spender -
<3>is usually AoE related and spammable -
<4>up for grabs, though I try to have either a backflip/movement or (self) AoE on this -
<5>up for grabs -
<6>always a potion -
<~>(tilde button) on US QWERTY is left of the<1>, this is always an interrupt -
<ALT+1~4>up for grabs, usually semi-frequent skills, anything with longer CDs -
<F1>always an essence -
<F2>something I use infrequently but still have to have a quick reach -
<F3>always health stones -
<R>movement speed related -
<F>either a panic defense or spammable defense -
<M4>usually a dispel or stun -
<M5>usually something I can pull with or a stun -
<ALT+M4>usually a (hard) CC of sorts -
<ALT+M5>usually a racial -
<M3>usually a taunt or otherwise situational skill -
<CAPSLOCK>rebound capslock to<NUM9>or N9 in the screenshot, up for grabs, usually a situational skill -
<Z>primary mount -
<SHIFT+Z>water mount -
<ALT+Z>transmog mount
List the spells you have assigned to these 19 buttons.
Im not gonna type out 49 Spells i have keybinded + the few on Ctrl i’ll be here longer than id like xD
49 Spells, yeah ok
? what you getting at
I was agreeing with you, it’s a lot to type out.
I have bound:
1,2,3,4,5,6,9,0
middle mouse, mwheelup,mwheeldown
q,e,r,t,f,z,x,c,v,`,capslock,space,f1,f2,f3,o,p,i
and I have shift, ctrl and alt spells on:
1,2,3,9,q,e,r,t,v,capslock,space,middle mouse, mwheelup,mwheeldown
That may be it. Any key that’s like “wtf how does he hit that” is bound to a button on my mouse.
In my head i like to keep things simple, i dont use any of the Lettered keys on my keyboard because i feel like it over complicates things.
Including ‘Mouse Wheel UP’, ‘Mouse Wheel Down’, ‘Mouse Wheel Left’, ‘Mouse Wheel Right’ And ‘Middle Mouse’ I use another 12 Keys on Mouse
Then ALT + All of the above
Then 1,2,3,4 on keyboard.
Then Ctrl 1-12 on mouse plus ‘Middle Mouse Button’ only.
For Random stuff like Focus target, Nearest Enemy, Character Sheet, i use F,E,C But im not really counting them as spells.
Just the thought of using “q,e,r,t,f,z,x,c,v” Etc. as some people have mentioned just feels off to me, your fingers must have to move all over the place, i think id be fat fingering all day long, haha xD
Thanks for all the help, im just gonna have to get used to Ctrl or Shift 1-12 i think.
How are these keys harder to press than 1 to 6? 
When you use wasd for moving (and also mouse for moving) your hands stay in that area of the keyboard.