Signatures are very different indeed.
I had HJE-900 for a year (2010) and I liked them very much, but it was obvious when I upgraded to FX700s how limited they were in terms of separation and mids. Treble were aggressive but could be tamed a little using Comply T-400 foams (also nice with Ts-400).
I consider Yamahas to be better in nearly every aspect except treble and build quality (but HJE-900 are built like a tank, it's difficult to beat).
The mid-bass hump is usually bad for clarity since it tends to invade the lower mids, isolation was average at best, even with Ts-400 providing a very good seal. Mids were clear but a bit recessed, and treble were forward but not very realistic (cymbals were drilling into my eardrums, so piercing).
Going from FX700s to EPH-100 was not such a shock, despite the differences in signature. Just few hours to discover what's missing in FX700: good mids and a touch up in separation. I could live with the loss in bass and treble quality, so well that I just sold the FX700s.
EPH-100 are also pretty forgiving with the music source.
Yesterday I was listening some old Queen recordings (A Kind of Magic and a few others) with my SE535LTD and I nearly puked. It was sounding so bad. No such problem with the Yamahas since they don't put instrument/vocals so much in your face.