It's been a while since I was last here and poked at some projects, but this should work, and you can use this as a starting place. I did change your 2.5 keys into 2.75 and adjusted the 1.25 down to 1.0 in order to make it easier. I didn't even know there
were 2.5 keys. I know that's not what you wanted, but I've attached all the relevant files so you can make adjustments.
![Dihedral 79 (80% Merged Ten Key board) 92676-0](https://geekhack.org/index.php?PHPSESSID=elc6uk4a3u7e4ff4auvsfo4nhks61eit&action=dlattach;topic=67948.0;attach=92677;image)
This should demonstrate how it could be built with the matrix provided. It's not the cleanest, the matrix is not exactly clean, since I jammed things in where there wasn't space... I was working from another project I was dabbling with a long time ago, and I just adjusted it really quick to be closer to your layout. There is an LED under CAPS and the center key/spacebar to use as... an indicator? Technically there is still one pin free on the atmega.
![Dihedral 79 (80% Merged Ten Key board) 92678-1](https://geekhack.org/index.php?PHPSESSID=elc6uk4a3u7e4ff4auvsfo4nhks61eit&action=dlattach;topic=67948.0;attach=92679;image)
Edit: I removed the zip file, because I realized that the diode footprints are old and wrong - I'll update it and post a new file back in.
Edit2: see
this post for the updated zip file.