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Originally Posted by
JohnnytheSkin 
1. When I calibrate color, should I use the native resolution of the display, in this case 1080p, and calibrate to the HD 709 standard, or the SD 601 of the source (a progressive scan DVD player and a Nintendo Wii)/
This really depends more on the display than the source. I think both of your displays had xy color points (CIE chart) nearer to 709, so if that's the case then just use 709.
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2. What light output should I aim for on an XBR1 SXRD and a XBR5 LCD? From Tom Huffman's guide, it seems 40ft-L for the SXRD and 50-60ft-L for the LCD...good? Should I go more towards the 50 or 60 for the LCD? My viewing will be during the day in a light controlled, reasonably dim room (not a lot of ambient light) and at night in a darkened room, and I'd prefer to find a happy medium.
This will probably also work for the LCD, but for the SXRD set brightness as low as possible so that you are displaying all information above black. When you set the brightness you can set iris to the max setting in order to see near-black bars if you want.
Once you have set brightness, then set picture as high as possible. When turning up the picture control your SXRD will probably run out of red. To see this happen do a continuous measurement on a 100% white or above-white pattern. As you turn up contrast you're likely to find that there's a point where red no longer increases along with green and blue. Somewhere in the area where that happens is around where picture should be set, but you might need to lower the control a bit below where red stops increasing to get a little more linear grayscale response.
By setting brightness as low as possible and the picture as high as possible that will get you the maximum contrast the SXRD is capable of. Once you have done this, then just set the iris to whatever you prefer (on the LCD you might want to set the backlight when setting picture and grayscale). A low iris setting might obsure details near black if there's much light in the room and a high iris might wash-out blacks if there's little light in the room. Personally I can't stand washed-out blacks so I use a lower iris setting, ignore the 100% white output, and limit the amount of light in the room during the day.
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3. Just how important is gamma?
It just relates how bright different shades are relative to other shades. Gamma is sort of like contrast in a way. Contrast tells you how much brighter white is than black, and in that same sort of way gamma can relate how much brigher say 50% gray is than black. A higher gamma would mean that for the same white and black levels 50% gray would be darker. If either Sony has any way to increase gamma it would be in the service menu, so I'd say to generally ignore it unless someone who is familiar with your TVs could tell you how to change gamma. You know how you were talking about setting 100% white to a certain level, well no one suggests setting 50% gray to a certain light output even though in my opinion 50% gray light output has more difference in the subjective brightness of the display.
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4. Should I calibrate the black level with a pattern, or using the .65% calculation? I did the latter before and could still see the grayscale, but was told my numbers were way to low (indeed my brightness setting was four or so below what most in the XBR4/5 thread are using).
For my SXRDs the percentage way doesn't work, so I would suggest using a basic pattern that shows gray shades near black and set brightness as low as possible so long as you're not clipping dark grays.