I think it’s not clear what you’re asking for…

Bembo Book come with two R's in all styles. One with a long leg and one short.

I know what you’re talking about. You don’t like Bembo’s long leg of R, so you’re trying an alternate, right?

It’s hard to tell, since the color of the new R can be slightly different from Bembo. I don’t know if it is a good solution, but why don’t you choose another font? I was thinking in Poliphilus & Blado. Same source of inspiration, no strange legs. Some other strange letters, though.

Oh, you are right, frode.

http://www.fontshop.com/fonts/singles/monotype/bembo_book_pro_roman/&s=c

There's no automated method of changing it, as far as I can tell, though. You should consider that.

You can change it automatically in any app that supports OpenType features by turning on Stylistic Alternates.

InDesign does not support Stylistic Alternates!

Ahh, yes, I forgot. What a pain. This is why FontFont puts its alternates in Stylistic Sets. Your only automatic option then, is to do a find/change on the Glyph level.