Here are a couple of thoughts (I am working on digitizing slides with a Nikon D800E and Olympus bellows and 80mm macro lens.
Your Omega enlarger may not be the best light source for the job for a couple reasons. If it has a condensor head, it is going to show dust and scratches on the film more that using a diffuse light source without any real gain in resolution or accutance (collimated vs diffuse light source issue). (I have done comparisons of digitizing with an Omega B22 as light source with and without the opalescent diffuser on the slide holder between the condenser face and the slide, and to my suprise the collimated light source did not improve the sharpness of my image, but boy did it make dust etc stand out.) So if the Omega is a condenser enlarger, you want to put a piece of translucent plexi or similar between the film and the condenser face. Also, since you are using an incandescent light source, in effect you are underexposing the blue channel which in theory could make the blues noisier. You could correct for this by filtering the light source, of course. [Edit: Ooops, just noticed you are using a light box for the light source!]
Second, calculate your reproduction ratio and pick the appropriate lens. For example, for digitizing slides with the D800E, the Olympus 80mm f4 or Rodagon D 75mm f4 are good choices because they are optimized for 1:1 reproduction. However, you are shooting 6 x 6 fim with a 4/3 sensor, so you might want to take a look at the Olympus m4/3 60mm macro lens which is supposed to be screamingly sharp across the frame and likely is well corrected for the magnification ratios you are shooting at (rough ballpark 1:3 or 3:1, I can never keep the ratios straight). Alternatively, perhaps a 80mm enlarging lens, that likely is optimized for around 1:4. The 50mm lens is not optimized for the ratio you're shooting at (it's likely around 1:10), so not the best lens for the job in any event. [Edit: just noticed you are stitching, so never mind...]
Oh, and while an LS9000 is a nice idea, make sure you're sitting down when you check the prices.