That's a nice-looking wagon and rather finer around the solebars than the Slaters' equivalent. Well done! Some notes follow in reference to your numbered points.
1. The 2FS people have a cunning device for scribing planks. It's a board with a guide fixed at a slope of (IIRC) 1 in 15 to the axis of the planking, against which slides a right-angled triangular piece that also has a 1 in 15 slope. Moving the triangle a known distance along the planking moves it 1/15 as far in the other axis, so distances between grooves can be set rather accurately. There's probably a picture over on the 2mm-Association site.
2. Also make sure that the solebars are to scale width. Most in kits are too thick, and the BB axleguards are already about a scale inch (shocking!
) over-width.
If using the BB brakes, I prefer to grind a little off the shoes to get clearance rather than tuning the wheelbase. I have a grindstone with a built-in arbour that is just the right diameter for this.
Having won clearance between wheels and shoes, I still find it difficult to fix the brake assembly in the right position to avoid binding. Hence those baseplate's I've been blathering about: they are an anti-cock-up device. I note that any end-play in the wheel bearings makes this much worse as the axle ends can move sideways in their cones.
3. If using BB "1907" axleguards, and if the bottom of your floor is level with the top of the headstocks, then you
should be right for buffer height with 0.5mm packing under the axleguard units. I've done this on most of my Slaters' kits and it always works. Note that "floor level with top of headstock" probably isn't how the MR built the wagons, but nobody will be able to tell without measuring.
4. I used regularly to mess up the vertical position of the V hangers so that they didn't line up with the tumbler in the push-rod assembly. I now make up the hangers and brake shaft as a soldered sub-assembly by clamping the hangers to a scrap of wood that is as wide as the solebar (1.5 or 1.6mm depending on how I've thinned the solebars). I can then clip the hangers over the solebar and secure them with the solebar in place on the wagon.
Check your GA for the shape of the inner hanger. Earlier wagons of the MR had a vertical strap there instead of a V-hanger. D299 is probably late enough to have a V-hanger.
5. You means downwards? I thought that the full-sized headstock was 12" deep, the solebars were 10" x 5" and the bottom of the solebar aligned with the bottom of the headstock, leaving the stop of the floor about level with the top of the headstocks. But I don't have the GA, so don't treat that as gospel.
6. 51L lever-guards are easier to fold than the BB ones (sorry Bill...).
7. Folding the joggle in the lever is hard. I always end up making it too deep because my smallest pliers are a bit too wide and my tweezers don't have the grip to do the bend. There is probably a need for a bending jig ... or possibly grinding down a special set of pliers. In 2FS, there is a freehand technique using two pairs of pliers pushed towards one another; I don't know if it would work with twice the thickness of brass.
Concerning paint, I have a warning (you and others probably know this, but just in case). The colour sold as MR wagon grey in the Precision range may be the wrong colour for 1902. It's a rather blue-green shade of grey and an associate on RMweb suggests that it may represent some ex-Admiralty paint that the MR bought cheaply ...
after WW1.