Providing the E6400 is updated to the V4.x software (which you can do if this is not already done) the only difference bewteen it and an E6400 Ultra is the beat monger feature.
I have both an E6400 and an E6400 Ultra and they are identicle in every respect and I freely pass banks and samples between them. The E6400 Ultra is fatser for long off line processing jobs but the E6400 is fast enough.
The only other advantages of the Ultra range is that it can take an internal IDE drive where as all previous models require SCSI. There are also some optional extras for the Ultra that won't fit in the original E6400 ( the software is the same but the motherboard is very different) but EMU still offer expansion parts for the non Ultra models.
$1300, well I am in the UK and that eqautes to about £850. Not a great price but they do go for that, if your getting a hard drive or anything like that then it is possibly a good price.
Emu will also upgrade your original E6400 to full E4 Ultra hardware. Basically they replace everything but the front of the case. Buying an old E6400 and getting it upgraded to an E4 Ultra is a cheap way to get your hands on a new E4.
If you don't need 8 outs but can make do with 4 then you could look at a new E5000 which is, again, software identicle to the E6400 Ultra but with limited outputs and upgrade options. I have seen them new for £999 in the UK.
What ever way you go the E4 and E4 Ultra range are fantastic.