I use a 90 mm (~ 135 mm) lens without problems, but dislike using external viewfinders, which I find slow and inaccurate.
For framing, I use the 50 mm framelines, and draw imaginary diagonals connecting the ends of the framelines: the diagonal centres = the corners of the 90 mm frame. See my website:
http://www.richcutler.co.uk/r-d1/r-d1_04.htm
I think using a 135 mm lens (~ 200 mm) is pushing the envelope:
First, it'll be hard to focus accurately as the R-D1's rangefinder mechanism can only cope in theory with f/6.7 or smaller for 135 mm lenses (see
http://www.richcutler.co.uk/r-d1/r-d1_05.htm).
Secondly, the view will be difficult to estimate in the R-D1's viewfinder because of (a) its small size and (b) the significant change in the field of view as the point of focus moves from near to far (analogous to moving your eye nearer/further to a keyhole).
An external viewfinder will be more accurate, but finding one that matches the R-D1, the 135 mm lens and adjusts correctly for parallax will be a pain, and even then the change in the field of view when focusing won't be accounted for.
Personally, I'd only consider using a 135 mm on the R-D1 as a telephoto lens, and would be generous with framing for safety's sake. I'd also keep very close tabs on my depth of field when it's getting shallow owing to the f/6.7 limit.