Switches to 10x10 matrix (20 free pins required for matrix, as opposed to 24 previously). This gives me all the pins I required including the flash option to store macros (plus one spare pin). 

Smaller keyboards with fewer keys probably wont have this issue. The STM32F4xx (48 pin) should handle a full size keyboard using a 10x11 matrix but that's for another time...

As I said previously, I'm building with the Blackpill to test everything prior to building with discreet components. Quite a learning experience, especially trying to route a 10x10 matrix, not an easy task on two layers, so I switched to four.

Of course I had to modify the code and keyboard_layout,json etc., but that bit is easy enough. Some more checking of the Kicad file, then off to PCBWay...

keyboard_layout.json (from: keyboard_layout_editor.com)

[{f:3,a:7},"Reset",{x:0.25},{"p":"DCS","a":7,"f":4,"fa":[5]},"Esc",{"x":1},"F1","F2","F3","F4",{"x":0.5},"F5","F6","F7","F8",{"x":0.5},"F9","F10","F11","F12",{"x":0.25,"f":3},"PrtSc","Scroll Lock","Pause"],
[{y:0.25,"f":6},"M1",{"x":0.25,"a":5,"f":5},"¬\n`","!\n1","\"\n2","£\n3","$\n4","%\n5","^\n6","&\n7","*\n8","(\n9",")\n0","_\n-","+\n=",{"w":2},"Backspace",{"x":0.25,"a":7,"f":4},"Insert","Home","PgUp"],
[{"f":6}, "M2",{x:0.25},{"f":6,"w":1.5},{"f":6,"w":1.5},"Tab","Q","W","E","R","T","Y","U","I","O","P","{","}",{"x":0.25,"w":1.25,"h":2,"w2":1.5,"h2":1,"x2":-0.25},"Enter",{"x":0.25,"f":4},"Del.","End","PgDn"],
[{"f":6}, "M3",{x:0.25},{"f":6,"w":1.75},"Caps","A","S","D","F","G","H","J","K","L",":","@","~",{"x":1.5},"V↓"," >","V↑"],
[{"f":6}, "M4",{x:0.25},{w:2.25},{"w":1.25},"Shift","|","Z","X","C","V","B","N","M","<",">","?",{"w":2.75},"Shift",{"x":0.25},"<<","↑"," >>"],
[{"f":6}, "M5",{x:0.25},{w:1.25},{"w":1.25},"Ctrl",{"w":1.25},"Menu",{"w":1.25},"Alt",{"p":"DCSSPACE","w":6.25},"",{"p":"DCS","w":1.25},"Alt",{"w":1.25},"FN",{"w":1.25},"Menu",{"w":1.25},"Ctrl",{"x":0.25},"←","↓","→"]

From keyboard_layout_editor.com my Ayla80 99 key version.

Note for above image: Might increase left shift from 1.25 to size to 1.75, then move \ to far right (before right shift) and reduce right shift from 2.5 to to 1.5. This might make more sense...

3D Image

New 10x10 matrix (20 pins) version