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.
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.
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.