What would I do if I were in your position? I certainly wouldn't take the Femara yet! I'm sure you've read on here that it can take a healthy couple up to a year to conceive. The only "issue" you mentioned was cycle length (I assume that means you have long cycles?) but even with long cycles, it's obviously possible you are still ovulating. Are you charting your temps to confirm ovulation? If not, you should check out fertilityfriend.com so you can be more aware of what your body is doing.
You said you've only been TTC for 5 cycles - I don't know if that means 5 months or more but is that the length of time you've been off birth control? If so, it can take quite a few months for your body to regulate itself after coming off BC so it sounds like your OBGYN is REALLY jumping the gun here and you shouldn't have even been referred to an RE at this point anyway. If I were you, I would not take the Femara, I would not worry about your right tube since the dye did eventually get through anyway, and I would try to relax and keep TTC naturally. I would also think about looking into seeing new doctors multiple months down the road if you're not KU yet.
If you do get to a point where you think about taking the Femara, make sure you read some of the threads on here about the meds and being properly monitored. It's no joke and can cause serious issues.