I have been renumbering a bunch of CR, PC and PRR MTL three bays for a Conrail coal train for the last few months. I chose the MTL cars over the Atlas and Life Like cars for the same reason you have. I have not gotten around to trucks and couplers yet, but I did experiment one day with one car to get an idea on how big a task it would be. First, Atlas 100 ton trucks and 36" FVM wheels made the car look very nice by lowering the ride height some. The problem was, the wheels hit the slope sheet. I tried BLMA 100 ton trucks, and I had to use an MTL spacer washer to prevent the wheels from hitting the slope sheet. This gave the best compromise between ride height and operation. As far as body mounts go, if you use MTL's, it's not going to be cheap. I used a 2003 assembled lid side down (slinky only when pushing). You have to enlarge the hole in the lid so that the screw is recessed. Otherwise, the wheels axil will hit the screw. An atlernative I have yet to try is the Atlas body mounts, number 23015 (no slinky). The screw comes recessed already. These will also accept McHenry couplers. This may be a good option since you are going to run them in unit trains, and if the coupler height is a little below the MTL standard, it won't matter except for the two end cars. Years ago, Unimates were available in a body mount form that simple screwed (the shank had a hole in it) to the car. As far as coal loads go, I beleive Hay Brothers makes flood loads. I don't need to lower the brake wheels, so I cannot help you there. I personally wouldn't bother, but that's just me. Good luck.
Jeff