I think you're on the right path, a couple of notes,
1) With a signal trace between two planes, the return current will split between the two planes, even if one of the planes is split. The return current cannot "see the future" and decide ahead of time which plane to return on. It will return above and below the trace until it sees the split at which point is says "oh crap!" and pays you back by possibly causing you to fail FCC testing. So you want to avoid running traces over plane splits even if another adjacent plane is not split. You can deal with splits with capacitors and such but this type of solution is less than ideal. I'd focus on always avoiding running a trace over a plane split on an adjacent plane.
2) Wide return paths on DC signals don't really matter.
3) You asked about two signal layers sharing the same plane. Usually, this is not a big deal if done properly. What many people do is use one of the layers as a "horizontal" signal layer and the other as a "vertical" signal layer so the return currents are orthogonal to each other. It is very common to route two signal layers for each plane, and use this horizontal/vertical technique. The most important thing to remember is to not change reference planes. Your setup could be a little tricky because going from the bottom layer to the 4th layer adds another return plane. More typical 6 layer boards are
1)ASignalHor 2)GND 3)ASignalVer 4)BSignalHor 5)POWER 6)BSignalVer
If you need smaller additional planes, like under the micro, these would usually be placed as an island on one of the signal layers. If you need to use more power planes, you might want to think about going to 10+ layers.
4) Plane spacing is important, and can have huge impact on performance, so you should specify this to the board house. If you take the example 6 layer stackup I mentioned above, spacing of .005 .005 .040 .005 .005 (instead of standard stackup with equal distance between layers) can make an order of magnitude improvement. It keeps the signal layers close to their reference plane (smaller loops).
I highly recommend the first thing you do is purchase High Speed Digital Design: A Handbook of Black Magic. Read it twice, then read it again :)
One important point. The crystal frequency doesn't matter here, you need to know the speed of the signals on the lines in question (which can be many times the crystal frequency). More over its actually rise / fall times that drive almost all signal integrity issues, not the digital frequency of the signal.
Designing for DDR isn't really that simple. High speed design can be a bit of a 'voodoo' art, even if you have $10,000+ simulation software. In other words, don't expect to nail the design the first time without putting in the work to understand the issues involved, a check list really won't cut it.
What I mean is, you really should start by reading the book I linked. It will give you enough background that the information in AN2582 will make sense (side note you linked the wrong pdf in the op). It will also allow you to understand the design trade offs you'll likely have to make when laying out the PCB.
That being said, here are my thoughts:
Routing Guidelines:
High level things to consider / avoid:
1) Route on a single layer, with a solid ground plane under it. Avoid vias like the plague. If this isn't possible, the DQ and ADDR groups are most critical, route those first, try to only move signals as groups to different layers.
2) Make sure you impedance match the traces: 50-60ohms, whatever comes out to the 'nicest' trace width for the design. Note the difference between differential and single ended lines and match the impedance appropriately.
3) Maintain proper signal spacing (i think 3*signal line width is preferred). This will help limit crosstalk between signals.
4) Match trace length of all related signals / groups (differential pairs, data bus, address bus, etc). Try to keep all traces to roughly the same length, that is you don't want the address group to be 1cm longer than the data group if you can avoid it.
5) Use source termination. You probably don't need parallel termination nor a Vtt given your board size and use of a single ram ic.
6) Pay special attention to Vref, it needs to be stable: well decoupled, fat traces. For a single ram module you can generate it with a simple resistor divider.
7) Don't use resistor banks for the termination, use individual resistors.
8) Expect that you'll need to 'play' with the source termination resistor values on the first prototype. Basically put a scope on the signal and try various values in the region of (trace_impedance - driver output impedance) = R. Look for the value that results in the cleanest signal (read up on eye patterns).
Signal Groups:
They are (NOTE: Taken from AN2910 and this is for a 64bit + 8bit ECC module, you don't have all these pins):
Data Group: \$MDQS(8:0), \overline{MDQS}(8:0), MDM(8:0), MDQ(63:0), MECC(7:0)\$
Address/CMD Group: \$MBA(2:0), MA(15:0), \overline{MRAS}, \overline{MCAS}, \overline{MWE}\$
Control Group: \$\overline{MCS}(3:0), MCKE(3:0), MODT(3:0)\$
Clock Group: \$MCK(5:0)\$ and \$\overline{MCK}(5:0)\$
Stack Up:
There are lots of ways to do this. Micron gives their recommendation for 6 layer stack ups with 3 or 4 signal layers in app note TN-46-14.
Really stack up is an entire topic of its own, but if your device has the 'standard' assortment of devices on it, these recommendations should work fine.
Other Stuff:
I think the rest of your questions are answered in the linked pdfs or AN2582. There is another checklist available in AN2910.
Best Answer
You can route across a cut up plane with no issues as long as each cut up plane is paired with a tightly coupled solid (gnd) plane -and- you engineer the PDN (bypass network) to have sufficiently low impedance between all power plane islands and ground (use something like my PDNtool.com for this).
If you make the cuts wider than about 1/3 the electrical length of the rise/fall time of your signals, you will start to see some reflections due to the lower capacitance. This can easily be simulated if you have access to an IBIS simulator.
Also the plane nearest to your stripline traces will "dominate", so if that is solid you have no issues either.
PS: Reference boards are not holy. There are MANY reference boards out there with lots of serious design errors. So watch out!
Does that answer your question?