1) Probably the easiest way to add off-route POI's, using the method here, would be to put them all in another .tpo file and then merge them into the main file with all the on-route POI's when you want to print.
2) Not that I know of. My diamonds are blue with blue lettering on white backdrop. The font size cannot be changed, to my knowledge, but the size is good for squeezing a lot of verbage into a small area on the map. Incidentally, sometimes the waypoint labels can run into each other, esp. where the route line runs more horizontally than vertically. When you're all done making changes to the csv and Data Book you can manually move any of the waypoints on the map in TOPO! so they're more visible. Although the waypoint coordinates will change in the program, they'll stay the same in the other resources, which is where you'll reference them anyway.
3) It's a lot easier to get the direction set before starting on this, by simply breaking the trail trace in two and then reconnecting it by clicking first on the broken portion that should come first in the new alignment (and then clicking on the other portion to reassemble). That's standard TOPO!-ese. If you've already run the process and need to rework both the labelled map and Data book, it's a little trickier. Honestly I haven't really thought through how best to do this, but would assume you could use Excel formulas on the csv file based on known section length in order to flip all the mileages and then reverse the order of the rows. Then in TOPO!, delete all the existing POI's and import new POIs via the csv. Ditto the Data Book changes, in terms of using formulas.
4) You can overlap map coverages for printing purposes, which helps to error-proof things as you move the selection box around. What I find helpful, though, is first to zoom out (reduce) to 50% (level 5 map) so you can see most of the selection box. In the dialog at right, under More Options, Magnification, I generally use 40% to 50% of original to minimize the number of printed maps while still preserving enough visual detail. Under Marginalia, select Grid Labels. Under 'Additional Settings' choose Lock Selection to One Full Page, and optionally, Snap Selection to Grid, which will avoid the need to overlap your maps by insuring that the edges are perfectly aligned.
I don't actually use TOPO! for printing, but just to save Bitmap images for later manipulation in PhotoShop (RGB to 16 colors, map numbering in the corners, etc.) So I'm not familiar with Rick's technique for printing consecutive maps. Normally you want to toggle between portrait and landscape printing modes based on the trajectory of the trail trace in a given area.
Keep in mind that the methods described in the PDF aren't really compatible with uploading to a GPS unit, since the POI labels on the map are intended to be descriptive (long). (And there will probably be many of them.) But you could build a parallel file in Excel that uses truncated versions of your waypoint names, maybe eliminating any characters that your GPS can't handle. Or perhaps some GPS units are able to 'take what they get' and just deal with it, I don't know. In any case, the waypoints probably won't be spot on, so plan to use them in a GPS with full awareness of the inherent inaccuracies that comes with software-derived (rather than field-recorded) waypoints. Not only that, but the POI's are just approximations anyway, tied to the nearest incremental waypoint in the TOPO!-created route. In any case, rather than uploading to a GPS, I would just plug waypoints manually into the unit as necessary (grab them from the data book entries).
All of this is fairly new-to-me, too, by the way, as I wrote the PDF as I was playing around with the possibilities. Hopefully there will be improvements to the workflow forthcoming, or somebody will point out something obvious that I'm missing. For one, it'd be nice, under "step 6" in the PDF, if there were a way to keep only your custom POI's and ditch the ream of additional waypoints without having to ctrl-click on each of the POI's individually.