The cowling has a notch close to the midpoint of the flange that goes under the outer case, which slides onto a standoff screw attached to the logic board. I used a Sharpie marker to put one "alignment mark" on the inner edge of the outer case. I put another alignment mark from the midpoint of the cowling notch out onto the visible part of the cowling. This made it much easer to reassemble, especially since my standoff post provided a tight fit, which, when I did this the first time, felt like "it doesn't fit . . . again?" It also helped to insert the end of the cowling closest to the heat sink first, which acted as a "fulcrum" for the cowling to "click" onto the standoff post.
During this process, I took advantage of having the logic board out, checked the BR2032 battery, which tested nearly dead, and I replaced it with an ECR2032 battery. If you choose to do this, be careful with the moving and replacing of this button battery. There is a wee-little directional arrow on the ( - ) side of the battery holder, which means move the battery without prying towards the positive ( + ) side. One end of the battery then pops up to grab. I also tested the new replacement battery before putting it in. I used an AMPROBE BAT-200 Battery Tester.
I replaced the two black rubber grommets with two white silicone ones. The white grommets were easier to see, and (whew!), they didn't catch and deform like the black ones did. I also used the "gravity technique" mentioned above, along with putting two T8 screws temporarily into the side holes of the hard drive closest to the logic board to use as "positioning handles" and guides to place into the "far end" white grommets. Being able to align much easier, along with controlling the hard drive, made for a much smoother replacement from my first adventure.
After struggling with this the first time, I laid the cables "more flatly" closer to the power supply, and then secured them with a piece of black electrician's tape. This made reassembly much more tolerable, by keeping these wires hugged close and out of snagging way. There does not appear to be any heat damage to the tape over the past year.
7 December 2015: Successfully used this guide on my new BTO Mid 2012 i7 13" - really nice to have this tutorial up on my iMac while I did this - nice to "check off" the steps.
I remembered from somewhere that one at least used to have to reset the PRAM/SMC, but, it recognized the new RAM amount of 16 glorious GB with no problem.
I think disconnecting the battery had the same effect, as the Date reverted not quite to 1969 - that also updated with no problem.