Admittedly I work with GRASS solely on the text-based side - rarely if ever 
touching the GUI - but hopefully I can help:

1) To be honest, it's probably easiest to continue to use d.his and then 
display the resulting map using the GRASS plugin - QGIS doesn't really have 
many (if any?) raster tools, while GRASS was created primarily to deal with 
raster features (and added vectors later).

2) I believe r.mapcalc is the way to do this on the fly - not sure what you are 
asking, because I'm sure d.rast calls this "on the fly" when you go to display 
the image?

You can always do something like
r.mapcalc "{$output_map} = if({$input_map[0,0]} >= 3000, {$input_map[0,0]}, 
so it doesn't stop the processing.

3. You CAN do raster reprojection on the fly. However, your results won't be 
anywhere near as "clean" as a vector reprojection as a result of the different 
format type. Also, there are some rules - I believe the projection has to be in 
the current region of the location you're reprojecting to, and also the 
resolution must be sufficient in order to handle the map.

The r.proj part of the manual has two good procedures for doing so:
(old version but should still be okay)

4) I think it's an actual limitation - I am assuming, for a categorical map, 
you would like say all cats < 10 to have a transparency but all cats >= 10 to 
not have a transparency? I'm not sure how to do this, if this exists - I'd just 
use r.mapcalc and display two different layers.

I hope I didn't misinterpret what you're writing, and hopefully that was of 
some help.


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