I made a small lame benchmark with the famous "AKsack.wav" 
Result (both with JIT enabled):
FS-UAE: 16:59
E-UAE: 1:24 min
As you can see, there is a huge difference in speed.
By the way, on the host system itself without UAE (Core 2Duo E8400 @ 30 GHz, Ubuntu 12.10), I get the conversion done in 0:06 min. This result is equal to a 2.5 GHz G5 under MorphOS.
I am not a FS-UAE + Linux specialist (I use WinUAE). The developer and many user are on eab.abime.net
Link:
http://eab.abime.net/support-fs-uae/perhaps someone there has a tip for you