We've done quite a bit of work with Juniper MXes talking to Brocade MLXes using OSPF. We've been bitten by MTU mis-matches and Jumbo frame issues and solved all of our issues to my knowledge. We're now running MTUs of 9100 ish (I forget the exact number) on our OSPF area 0 interfaces on both Brocades and our MXes.
I haven't done any work with VPLS between Brocades and Juniper MXes.
I'm about to head out now but feel free to email me tomorrow on email@example.com
if what I've been saying sounds useful and I'll try and help.