Answering your questions in reverse order:
Originally posted by S E Scott I have seen images from the 645D that give the colour and look that I am after but I am also aware that there are split sensor issues with this camera and I do not know if these we ever satisfactorily resolved.
I personally have not experienced this problem however - I'll point out to you than other manufacturers ( i.e DALSA) also stitch sensors together, and there have been issues with them in the past but statistically few have experienced any problems.
Originally posted by S E Scott However, after much searching on the web, I believe that I see a significant difference in the colour rendition between these two cameras.
I would chalk that up mostly to the style of image processing the photographer has used - the 645Z has a
massive dynamic range, even bigger than the classic 645D. I will also state that the design of the CFA may be causing the differences between them. The only way you could make such a call is to get both a 645D, 645Z,your Leica M9 and do a straight comparison - and from there decide which you like the most**.
Originally posted by S E Scott As a landscape photographer it is vitally important that I am able to capture the subtle "pink" tones of the early and late light.
The colour gamut of Film Vs Digital is a rather heated topic, but my personal opinion is that if you use ETTR, you can improve the colour accuracy and rendering of complex and delicate colours - however with this technique extreme precision of exposure is required for this along with tedious profiling of your camera*,monitor,and printer to achieve the results that you are aiming for.
Originally posted by S E Scott To my eyes, the best and most film-like results came from my Leica M9 but I do not like the 3:2 format for composing landscape images.
The Leica M9 uses a CCD sensor from Kodak - who if you remember from the film days always put a distinct priority on colour rendering. The 645D also uses a Kodak CCD and produces images that are in many ways similar to the M9 - albeit with considerably higher resolution.
* Any filters you use should also be carefully checked for neutrality.
** Though personally, I'd say comparing Pentax lenses to Leica M glass is a bit unfair. I'd suggest you also try the Leica S2, which has the
best lenses currently going for a medium format camera, Pentax lenses render things differently from Leica lenses.