I realise that the E3 is almost entirely irrelevant these days, but just in case anyone wants to get one working...
I recently pulled mine out of storage and tried to put Debian on it. (I want to use it as a modem.) Unfortunately PBL wouldn't handshake. Investigation showed that at baud rates of 57600 and above, the E3's serial port seemed to be unable to receive data reliably, getting frequent single-bit errors. Transmission seems fine.
I eventually managed to get everything working by dropping the baud rate to 38400 (uploading the kernel and initrd takes an *age* at that speed), and everything works now.
This might be age-related; my E3 is now years old. A flaky capacitor causing the pulses to get smeared so that the UART isn't registering them properly? This seems particularly likely given that I don't have a level shifter, so I'm driving the UART at out-of-spec voltages. Alternatively it could be clock drift, but given that the UART is on the processor this seems unlikely.
So if anyone has an E3 which won't handshake any more, try lowering the baud rate and seeing if that helps. (pblq has an option for this.)
...
Incidentally, I don't suppose any of the uboot patches got accepted by upstream, did they? Editing the environment with a hex editor is slightly harrowing and it'd be so nice to have a version which could store them in NAND...