The recent build I mentioned, oh I suppose I should drop in a (poor) picture of it;

the memory bus traces range from 408 to 1337 (nice) mils in length, also with the CLK going double back to a return pin (I guess so the controller can estimate propagation delay itself?). Probably the return clock wasn't necessary at this bus length, and can be returned at the controller.
I don't have a scope quite fast enough to measure the full waveform, but from what I can see, the waveforms aren't noisy (supply is quiet), have modest overshoot (about 20%), and little ringing. Likely a consequence of the high trace impedance combined with pin capacitances, and the pin drivers being typical CMOS strength (30-70 ohms). (I measured CLK with a 10x lo-Z probe, which will have some damping effect compared to the ~100 ohm traces; again, 2-layer board.)
I don't see much conducted from the cables, and as you can see, the memory is off to the side, completely surrounded by stitched ground pour. Supplies are well bypassed (there are three 0.1's on the RAM, and three nearby on the controller's VCC and VCORE pins on that side). Ground is nearly solid, with exceptions made for traces crossing to the far row (including the CLK return signal), and VCC. There should be very little way for noise to go anywhere, even though it is quite a noisy location as attested by the near field probe.
Layout:

Top and bottom, transparent

Top alone

Bottom alone
Notice VCC comes from the corner of the controller chip, and "uselessly" switches layers under the bus (which happens to be most of the DQs), allowing ground to fill underneath.
I'm sure I could've optimized the bottom side routing better, perhaps even pouring ground between every trace, not just pairs. Breaking up the large group, the four parallel traces (half of which happen to be CLK!), would be nice. But of course, how nice that is, depends on how much it really matters; clearly the circuit is functional, and beyond that, I don't have much more I can test. (Perhaps the overshoot is triggering ESD diode conduction, perhaps it's causing increased current consumption, or stress, I don't know. I'd need much fancier test equipment to figure that out.)
There is a bus running around the SDRAM, just out of view, but you can see corners to the bottom-left and bottom-right. These of course would not be a great idea to route under it (but on a 4-layer design, that wouldn't matter).
Keep in mind that,
1. We still have not confirmed why and where the noise is being conducted on your board (incomplete testing information);
2. Multiple changes have been proposed, all of which are expected to have some effect on performance;
3. You have approximately zero intent of checking all of those proposals individually -- at least I'm guessing you aren't going to spend months, and tens of thousands of dollars, testing a prototype for each change.
It is quite possible that your initial change has already solved the problem to an adequate degree, and all the rest of this is just masturbation. (Which makes this a good kind of thread for people like me to brag about our glossy routes and stitched planes, but not a very productive thread otherwise...)
Tim