This is a very interesting thread.
Okay, looking at the PC Wizard results and at your camera pictures, I think I have an inkling of an idea of what is going on, at least indirectly. I don't have any idea what is actually directly
causing this, but perhaps if I throw something out there it will start other people's wheels turning.
First, even before I saw the posted PC Wizard information, I noticed in the pictures that you provided that it wasn't JUST a simple matter of part of the image being cut off. Initially, based on your description, I thought that you meant that anything beyong the gray line that you drew in Paint on your first posted screenshot was not displaying on the screen. However, the pictures you took with your camera show that the entire screen is being used up; there isn't a part of the screen that is "unpainted." The only way that this could be is if the image that IS making it onto your screen is being STRETCHED horizontally. And I think this is exactly what is happening! Didn't anyone else here notice that in the part that IS being displayed, the proportions look completely wrong? Look especially at the IBM boot-up logo.
The information provided by PC Wizard gives us some more clues, and in fact I think backs up this theory. First, please just ignore the "Video Modes Supported" section; on my T60p's UXGA display, it shows the same thing (1024x768 is the last listed resolution), even though it obviously has a greater range of supported resolutions than that pitiful list. What is more important, I think, is the "Maximum Resolution" listed. This should not reflect the maximum resolution supported by your video chipset, but the max. supported by the panel!
On mine, Aspect Ratio shows 4:3 and Maximum Resolution says 1600x1200 (the native resolution of the panel). Yours, on the other hand, shows an Aspect Ratio of 16:10 and a Maximum Resolution of 1920x1200! Your graphics chipset for some reason thinks that your panel is a widescreen WUXGA panel!
This would completely explain everything. It would explain both why things are being stretched out and why a part of the image is getting cut off: it's trying to take a 1600x1200 image and "stretch" it out to fit a 1920x1200 screen, because that's how many pixels the graphics subsystem thinks you have. The difference between 1920 and 1600 is 320 pixels in width, and if you create a 320-pixel-wide bitmap, it looks to be about the size of the area of your desktop that is getting cut off.
Now, WHY the integrated Intel graphics thinks that your UXGA panel is really WUXGA, I have no idea; I don't know enough about the way the graphics system probes the panel or how it is supposed to interpret the results or any of that. However, some part of that whole process is broken on your machine. I noticed that PC Wizard did not supply a manufacturer ID for your screen and that it calls the screen model an "MS_0003". On my T60p's IDTech UXGA display, the values that show are "N150U3-L01" for Manufacturer, and "LEN4046" for Product. It's also possible on some older IDTech displays that IBM changed the vendor and model information that the panel reports to something else; the same model panel in a T42p reports "IBM" for manufacturer and "IBM1A5D" for product even though all of the other status show the same values as my T60p. Either way you look at it, MS_0003 is not a valid ID for this panel, so either the Intel chip isn't getting a good response from the panel or it is not faithfully reporting back to PC Wizard what the panel told it about itself.
It COULD be that the Intel graphics are just not set up to support UXGA. I hate to tell you this after the fact, but perhaps the SXGA+ (1400x1050) 15" screen would have been a better option for you to look into since we already know that they have been paired with Intel integrated graphics in some R-series models. The pairing of a UXGA panel to Intel graphics is completely uncharted territory; Lenovo never did it in any model they sold. Even DB2DUDE made it pretty clear in his post (linked to earlier in this thread) that he installed his UXGA screen on an R-series with discrete ATI graphics since the "hack" he did to make it work properly relied on a feature in the ATI driver for X. Didn't sound to me like he had any experience with Intel graphics in his post.
However, all of that having been said, there MAY be a workaround to your problem that I think is worth having you try.
The fact that everything that is ever displayed, regardless of the resolution that it is being displayed in (for example, I guarantee you that neither the IBM boot logo nor the F12 boot menu are natively 1600x1200!), is being stretched off the screen probably means that the screen expansion setting is toggled on. In this mode, the graphics chip will try to take any image regardless of size and pixel-double the image until it fills what it thinks
is the size of the panel. At least on ATI-based ThinkPads, this feature is able to be turned off; with this setting off, an image smaller than the native resolution of the panel will be reproduced faithfully without pixel doubling or stretching of the image by placing the image in the center of the screen and allowing for a black border of unused pixels to surround the image.
Given that, out of the 320 extra horizontal pixels that it thinks your panel has, all 320 of them that are lost are being taken exclusively from the right side of the image (instead of half of them (160) disappearing off of the left side of the screen and the other half off the right side), it makes me wonder if you could solve this problem by simply turning off screen expansion, if such a setting is able to be toggled on Intel graphics ThinkPads. On discrete-graphics ThinkPads, this can be done in the BIOS; look for the "H/V Expansion" setting under Display, set it to Disabled, and save the settings. With any luck, even though the Intel graphics system will still think that you have a WUXGA panel, it will (hopefully) not try to "center" a UXGA image on the "virtual" WUXGA canvas it thinks it has to work with, and just start painting the image at the very first column on your screen.
The other possibility is that turning off this option will make the proportions look correct, but it will still "shift" the image to the right by 160 pixels in an attempt to center the un-stretched image on the display that it THINKS you have, which will leave you with a black chunk of unlit pixels (160 in width) on the left and 160 pixels of the right side still "cut off." If this happens, at least this will confirm the theory of misread/misinterpreted aspect ratio and native screen size.
Let us all know how it goes!
P.S. -- It might also be interesting to have you re-wire up the XGA panel again and run PC Wizard on that panel, just to compare it to the results you got from PC Wizard on the UXGA panel.