Like I posted before, the animators are too inconsistent with the portrayal of Mio's bass to get an accurate estimation of what model it is, exactly. Remember when they drew a Fender logo on Yui's Les Paul?
Consider the finish, for example. The intro alone for the 2nd season shows the bass in both 2 and 3-tone sunburst.
However, I guess the closeup 3D render of her bass DOES carry a bit more weight canonically (making the 3-tone sunburst the real finish, too).
From what we can see, it has the deeper-threaded bridge saddles like from the post-1959 to 1969 Fenders, which makes sense considering when the Jazz came out. However, it seems only the US-pickup-equipped MIJ basses have this vintage bridge on them.
Also, the bass has a copper grounding strip under the bridge like the 1960~1962 Fenders.
In the ending theme, the bass's headstock lacks any sort of serial number besides the Fender logo, a characteristic true of Japanese Fenders. (wish they added other parts of the logo, though. No real Fender has a headstock exactly like that

)
From these facts alone, my best (stupid) guess is that Mio's bass is a US-pickup-equipped Japanese '62 RI.
Therefore, the body wood is Alder!
Hope this helped.
But oh god, you're making me GAS for the Mio-signature bass, now.
Better not be Lazy and get a job while I'm at it...