Don't use a protoboard for high precision stuff. You need a solid ground plane, good decoupling, etc. The LTC6655 datasheet has a lot of information about the recommended layout, and they also have a demo board with full schematics, BOM, and layout that you can reference.
I laid out a 2" x 2" 2-layer PCB for mine and had it fabbed at OSHPark for about $20 for 3 copies. Add in $4 for the regulator, $15 for the reference, a few bucks here and there for decoupling caps and headers, and you're looking at about $100 out the door for three of them, or $50 for one.