How do you feel about the FC660C's feel compared to your HHKB?
I've now used FC660c quite a bit now. I'm not sure how reliant you are on the arrow cluster but either way, I would say that the HHKB provides a more efficient and versatile layout for me. Even working from the command line (linux), the HHKB function layer is more intuitive and to be honest, FC660's primary arrow cluster only helps me when doing excel sheets. Both boards make for an easy transport so that's not a problem, just that the FC660c is a bit heavier due to its plate. FC660c does have a noticeable clack on the upstroke so it can be disruptive in a class setting. Unless you want to silence it yourself, this is key for you since you mentioned that you'd use it in class. I don't have the Type-S but i'm sure it's not as disruptive, if at all.
There's more in regards to their embedded function layers but I would say, go with the HHKB. If you can afford teh Type-S and want to type in class, this is the best bet (and a safe one, lest you want be kicked out!). Also, HHKB will sell faster than FC660c, I think. Also, the HHKB thock is almost orgasmic at times. And I'm not even kidding bro.
I just brought mine into work today for the 1st time and I love it. But everybody says the same thing... Man that is tiny, WHY?!?! Because it's sweet and you suck! But I really like it, got the stock Pro 2 in black, about to pick up the Type S very shortly.