So, my character (a Chiss Technician/Engineer type), has this idea for building an astromech out of various other parts, and is envisioning the following:

A Viper Probe Droid head
A round R2-ish body
- some kind of 'neck' interface that would allow the above to level out on tilt
T3 style arms, with a forward lean (rather than the R2's backward lean)
A CP style third limb (wheel)

The main problem with the above, is that the Probe Droid's head would be ridiculously big on there, hence the thread title. Is there a smaller sized Viper Probe Droid out there that might work?

Also considered a Probe Droid head on a Dwarf Spider Droid body, that was somehow modified to fold up into an astromech socket when needed...

Yes there is, you just invented it. There are millions of different droids in the galaxy, it would be futile to trying to write an encyclopedia about everything in the star wars galaxy, because our planet is not big enough for that. ;-)

Besides it is very likely that the viper probe droid series has some even smaller versions, most likely for urban searches. Besides I am not even sure if the Dwarf Probe Droid is not actually fitting rather well onto a R2 body.
http://starwars.wikia.com/wiki/Dwarf_probe_droid

Just make it look however you want, and whatever size. The cosmetics of the design are just that, cosmetics, and droids are incredibly modular in their design.

In the canon Star Wars Battlefront 2 from EA the main character has a miniature probe droid that folds up into a disc and mounts into her back like a backpack. It’s a ID 9 or something. I’m sure you can look up the details.

Nice... Thank you for that. Looks like the ID10 is what you are referring to (with the ID9 showing up in Rebels).