I seriously think that you can't go wrong either way. At this time, MM and EB make the best basses for the buck on the market. The SR has a great tone and is very playable. It has a "classic" distinctive look and is VERY road worthy. The only knock I can think of is that it is very 1 dimentional compared to the Bongo's sonic output (I know that is overstating it a bit, but is the simplest way to get my idea across).
The Bongo on the other hand also has a distinctive look, but it almost has to grow on you, it also has a satin finished neck (I perfer a stripped down SR neck - nothing like naked wood!). The B5 is a little "end-neck heavy" and both are not as comfortable, IMO, as the SR. The road worthiness has yet to be tested - but then EB's customer service rocks! But then there is the matter of the extra pup. For me, that was the huge deciding factor. There is just so much more you can get at.
Another thing that is worth mentioning is that with the double pup Bongos, the spacing to the neck edge is rather small - making it harder for slapping (or it will make you a better player). But to counter that, the Bongo is a 24 fret neck as opposed to the SR (bass players are suppose to use those frets above 12??? Go figure

- I was thinking of custom ordering a 2 string Bongo (B and E) with just 12 frets

)
I have owned 2 SRs and sold them long ago - I loved them, wish I hadn't sold them, but now I am onto Bongoland (and I am happier for it).
In the end, it is your decission. Gather your info. Search these forums. If you can, go play them side by side. But whatever you do, think long term. Ask "is this a bass that I am going to be happy with" (there is nothing worse than buying a bass, and selling it a year or two later because it didn't fit your needs or expectations - trust me, I have done this several times).