I decided to put a brake on my 26" Kris Holm frame. I bought the frame new in March 2010. The current wheelset is a Nimbus 36H hub with a Large Marge Downhill Rim (also 36H). I was expecting to have to grind down the outer edge of the frame due to the brake rotor bolts according to the documentation with the Spirit Cranks, but there is quite a bit of clearance there. The rub is occuring between the spokes and the inside of the d’brake. Apparently I am going to need to remove some material on the wheel side of the d’brake (This is the word side of the d’brake on an external disc setup). It is not a constant rub, so it won’t need to be much material. Has anyone else came across this issue? If not, then I assume it is due to the Large Marge Rim causing the angle of the spokes to be different than with a normal rim.
That is a very strange issue. You might want to double-check that you don’t have under-tensioned spokes as it can affect how the rim is centered. I thought at first that your rim might be off but the Large Marge is hard to damage that much (except if you rolled over your muni with your car).
And another thing you might want to play with is the IS adapter you mounted on the D’Brake and the bolts that connect both. The IS adapter should not be on the side of the spokes and the attachment bolts maybe mounted the other way to increase the clearance on the spokes side.
If nothing helps, try to post a pic of your setup at the point of rub. It might help identify an issue before starting to alter the D’Brake 
Not so unusual actually, I also had the same problem when I recently built up my son’s KH 26 with Spirits.
The issue is that in order to get the cranks onto the spindle far enough for them to be “tight”, there can be tolerance issues with the D Brake.
I ended up grinding the D Brake down to clear both the caliper (using a 160mm rotor) and to clear the spokes/hub.
Perhaps the Mountain Uni caliper mount is narrower??
You could try increasing the thickness of the spacer between the hub and bearing, but keep in mind that this may mess up your caliper to disc alignment and/or make it so that the Spirits are no longer tight on the spindle.
A KH frame with caliper mounting tab is the best bet OR use an Oracle frame, a steel frame, etc…
I have had no problems with using a D Brake on my steel frames or Oracle frames. I think the issue with KH frames is that the bearing holders are exceptionally thick, so they “take up” a lot of spindle.
SV, I appreciate the suggestion although it is the d’brake itself that is rubbing. The IS adapter is certainly not on the side of the spokes and is in no way touching them.
Ben, thank you. That is what I thought. I will grind away some of the d’brake and that should alleviate the problem. While we are on the subject, what did you use for spacers between the d’brake and IS adapter on your son’s KH to align your caliper with your disc? This is your fault anyway! I couldn’t resist picking up a pair of those shiny new Spyres that you were sporting on Saturday. I am a recovering Gear Junky and am highly succeptible to relapse 
metric stainless steel washers, very thin, I think they have them at Lowe’s.
Depending on the fit, I have used washers to adjust caliper angle, caliper clearance over the rotor, and for caliper offset. You may also need to adjust the crank spacer depending how close you are on caliper alignment…
I have fewer problems with hub mounted rotors because they are not affected by crank fit, crank spacers, etc… but I prefer crank mounted rotors because the wheel are stronger and because I can use a 32h rim.
Isn’t there an oregon 32h hub?
Remember, the Oregon hub is “extra wide”…so they don’t work on standard unicycle frames.
Yes, but it is the wide hub, not the 100mm version. The 100mm version doesn’t have a mount for a brake rotor.
Beat me to it:)