Are you sure you have the negative centered in the negative stage? From the scan, it appears off center. When using the negative holder, the locator pins will assure that the negative is in the center of the projected area.
I'm not sure how you'd center with your homemade glass holder other than checking visually.
Chuck, this seems to be as much a product of the carrier as the lens. On mine (with the square bottom bellows) the negatrans tends to vignette on the right top and bottom when there is not enough clearance to the top, and on the bottom with the glass carrier. Not much, but this is where it will first show up with a 135mm Nikkor. No problems at all with the 150mm. Optically, the negative is centered.
There is only a slight difference between the condensor and diffuser head diameters (6 3/8 versus 6 1/4" respectively) The thickness of the carrier can play a role also. If you are working toward full-frame, I might suggest trying an 150mm and seeing if that solves your issue.
There were a couple of designs for the Schneider and Rodenstock 135 lenses. I remember that one of the designs was older and did not cover as the more modern design. I have the most modern 135 Componon-S, and it cover the 4x5 neg just fine. ( It is used on a Saunders 4500 enlarger.).
Maybe you should post what the 135 looks like, and maybe someone can tell you if it is an oldie... like a chorme lens rather than the more modern all black lenses....