The 40D was among Canon's first Live View cameras, also I see that it has separate R,G,B histogram during image review in addition to luminance. I consider these essential features for IR photography. (from many years of frustration not having these features in an IR body). I strongly recommend not IR modifying the 20D. My extreme frustration with not having Live View and RGB histograms comes from using an IR modified D60 (not 60D), very similar in vintage to the 20D. an IR 20D will certainly yield frustration in out of focus images that are over exposed. That being said, I notice that the 40D has an older LCD with only 230k dot resolution, whereas modern Canon dSLRs (even entry level) have 1.0m dot LCDs. This lower resolution screen may often be insufficient for accurate manual focus adjustment.
All zoom lenses will change their IR focus calibration upon zooming, so you can only AF calibrate one lens at one zoom position. Calibration at other zoom positions is a guess. Remember the red infinity IR focus marks vary lens to lens and with zoom position? On my older Canon 24-70 f2.8L this IR calibration changes markedly from 24-70mm at infinity distance. So even with the 40D and your calibrated 17-85, AF may be off depending upon zoom position and subject/camera distance. If you are really not interested in Live View/tripod for manual focusing, then bracket at -2.0 EV and focus bracket as well. Also use for f11 and smaller apertures will help to minimize AF calibration errors, but not the over exposure of the red channel. Thus you will shoot 9-12 shots to get one to take home (maybe).
Remember that phase detect AF uses visible wavelengths to AF, and will inherently be off for IR modified sensors. For recent cameras with a Live View you can use Live View "Live" AF, which is contrast detect AF. This will work as the sensor itself is used for AF. Sadly the 40D predates this contrast detect AF feature and it is only available on the more recent bodies.
Needless to say Company B is unrealistic, as the camera body can only be AF calibrated to one lens at one subject distance, unless you get a model with micro adjust. Micro adjust can help to calibrate AF from lense to lens with a given body. Even then those are small AF adjustments, and IR focus calibration may exceed this MA adjustment range. Manual focus with a high resolution Live View is the only guaranteed accurate universal focus for IR.
As for RAW conversions, don't you have DPP that came with the camera?
Just to show you it can be done with my older D60. As I recall this was hand held as I was standing on a log sitting in this large puddle.
http://www.fototime.com/C03ACD0A9DE2086/large.jpg
shot with IR modified D60. Many shots were taken to get one good one. However its much more productive to use the right tools.
http://www.fototime.com/0EB3CE9D5C33618/large.jpg
Paper Crane Tribute to Manzanar
IR Modified 5DII with 24 TSE II lens. RAW converted 3 times and various conversion areas blended. Used magnified Live View with external monitor to fine adjust both tilt and focus. I am happy with the 5DII feature set for IR.
Mike K