I'd set the basics such as white point and select the nearest gamma. Then, depending on how far things are off I'd work on correcting a bit via the projector if it is possible without artifacts - you can use the Spears and Munsil disc or Ted's to evaluate for anomalies in the ramps such as banding. I dont have a Lumagen, just an EEcolor box so I don't know about the Lumagen controls. Typically the advice i see is to correct whatever is possible at the projector side, then use external CMS/greyscale to sort the rest as best as possible before performing a 3D Lut calibration. The further things are off before you start the LUT, the more patches are needed to get lower DE average .
I have an DLA-HD990 as well. It has taken me a few days to figure out how to get round some of its CMS issues. Have found a steady medium I am working on right now, which is to boost the color setting so that the 10-75% zone does not end up being too non-linear in saturation when making CMS changes. Without this, calibrating for either 75 or 100% stimulus/saturation results in errors up and down the scale. Same goes for blue and Magenta. The side effect of the color setting boost is that yellows end up over saturated but the DEs are close to 3 and the luminance is good so I can live with that. There are also some issues with the color setting that can result in artifacting in certain reds - there are zones of the color setting scale that do this for some reason. It's not the easiest projector to calibrate - even tho it can drive beyond the 709 colorspace hard, the entire gamut is pulled towards green. One has to work on getting hues etc as close as possible for the entire scale before creating a 3D LUT. Without doing that first, the resulting LUT can introduce more errors than it corrects (even with 4500 patches).