Recently, I have been reading Fumon Tanaka's "Samurai Fighting Arts". In one chapter, it explains that koryu show acheivement by menkyo, while gendai arts use ranking systems and titles such as "hanshi". This confuses me because Shimabukuro-sensei is addressed as hanshi and I was under the impression that MJER was koryu... what am I missing?

That is interesting. It could be some people have very strict definitions of koryu and if an art doesn't meet them they can't be called koryu. Also arts change so maybe Shimabukuro-sensei has added the use of the titles for his own reasons or they were added before and he uses them.

The commonly accepted rule of thumb for koryu pertains to the founding date of the style. Founding before the Meiji Restoration is considered koryu, after is gendai.

While it is true that many, probably most koryu arts do not use the dan ranking system, many have adopted it.

All generalizations are wrong. Probably even that one.

Some would argue that the adoption of the dan ranking system somehow converts an system from koryu to gendai, but that just seems foolish to me. Assign a number to each of the different menkyo system rank levels and you have essentially converted those ranks to dan ranks. They are all general representaitons of skill and experience(not necessarily the same thing) and only mean what the grading authority decides they mean.

There are of course many branches of MJER with different grading authorities. Some use the Dan ranking system, some use a form of the menkyo system, some use both.