I understand what you're saying about Lightroom versus Canon's software. The latter can be a little kludgy. I actually use four different software to tether, depending on what I'm shooting. My favorite for still-life is a PC only called DSLRemote from Chris Breeze. At this point, it's the only software that allows you to do test frames without actually capturing an image (it's a preview test only). Quite handy, and something no other program does (although EOS Utility version 2 did, but has been removed from version 3).
You may be able to find a 1Ds3 for around $2000-2500. I sold mine recently for a fair price $2150, in hope Canon will come out with something new in the next decade. If you are willing to go with gray market, a 1Dx can be had for around $4500. I would still suggest going with newer technology if you can swing it. My 1Ds3 was 6-years old, in excellent condition, well maintained by Canon, but I frequently would rather have shot with my 1Dx. A 1Dx body will serve you well for the future, and especially if you are going from the 1Ds2, it will be a quantum leap. You may have a 5-year old computer now, but that won't always be the case. The newer Mac Pros utilize USB 3 as one of their connectors (as do the notebooks). My suggestion is future-proof yourself as much as possible, since things always improve and always advance.