Just examined my V35 and the only thing I can think of is the helicoid directly under the neg stage is off. This is presuming the neg carriers are not out of whack since you've already aligned this.

I'd be very curious to know how it works out as I've always considered these enlargers rather indestructible in spite of the precise build and tolerances and many parts. They were tough enough to survive newspaper use day in and day out by lab techs and hurried photographers on deadline which is one reason why I love using mine.