I tend to keep my MH lights ~6" above the water surface. It's far enough off the tank that it allows light to cover the whole tank, but not so far away that you waste a lot of light. MH lighting for a 40 gallon tank is hard because of the tank dimensions, but I've done it before. Because a 40BR is 36" long, it's hard to get light evenly across the tank, but two low wattage MH (2- 150W) bulbs will cover it. You'll get 7.5W/gal, enough for any SPS, and even light coverage. I suppose you could do something really cool like keep the light closer to one side and do a rock slope with SPS on the high light side of the tank and lower light corals progressing to the darker side. It'd replicate a huge water depth difference in nature in a relatively small tank.
Steve you have the same thing I just upgraded from, I didn't cover the tank at all to get max light. IF your tank has a brace in the middle you will want a parallel reflector so you can have the lights and reflector going the same way as the tank. What I did was something similar to what Mark suggested. I had the MH a bit off center that way the light could get under the brace as apposed to having a heavy shadow right in the middle of the tank.....It worked well for me for years.....I also had the lights about 6'' off the light.
pfo makes a nice reflector that might help, if you can dIY or have a friend help out.
i used two of the 24" PFO parallel with wo 175 watts MH and its works great. i know the 36 " can have 1 or 2 MHs mounts i believe. the price is right for those reflectors!
i did mine around 9 " off the water. glad i did, those refectors put out.
i do not run a glass or anything between the tank and lights. most of the makers or SE bulbs, check with you SE making, have an outer jacket of UV glass that can stop most of the harmful UVs from the SE bulbs. DE do not have that out jacket and should have some types of UV glass to protech your corals and fish.
picture of the ones i used