I was having trouble getting to sleep last night, so I finished placing the remaining components on the Scratchpad board. Here's a screenshot:
With plenty of free space on the board I kept the components making up the various functions grouped and separated. The DRAM array is pretty obvious. The row drivers are to its immediate right, column pre-charge above and column sense and mux below. The control and data busses are below that (on the bottom of the board, shown in blue), and the write data latches below those.
Outlined on the right edge of the array are the row read and write enable drivers, and to their right is the 3-to-8 row address decoder. Continuing to the right is the 3-bit refresh counter, with each bit outlined. Bit 0 is on the bottom and bit 2 is on the top.
The other groupings are logic functions to generate various signals such as read and write enables for the odd and even nibbles, row read and write strobes, etc. When placing these groups I worked from the output drivers back toward the input signals. I started laying them out left-to-right, but after finishing them I decided they'd work better with each group rotated 90 degrees clockwise. Originally the order of the groups was the same as in the schematic, but I've since rearranged them into what seems better from a signal routing perspective.
Speaking of routing, I also routed the refresh counters and the row decoder logic. This seemed to be the easiest way to be sure the layout was workable. There's still a lot of routing to be done: there are 639 signal airwires, plus 424 ground and 84 VDD airwires. I also need to add power decoupling capacitors, and decide whether to add provisions for charge storage capacitors in the DRAM array as I did with the IP board.