I think the closer you can track keywords the more money you can make.
I run daily/weekly/monthly reports for all my keywords and what type of cost per lead/acquisition they are generating.
Terms that are costing me more than my target I lower the bids and/or tweak the ad copy to create a more qualified click.
Terms that are well below my target I typically up the bids (if i'm not already on top) and tweak the ad copy a bit to see if I can increase the CTR (be careful with this though as you may ruin your cost per lead).
For a 20,000 keyword list I realize creating 20,000 tracking IDs is just not possible. I would imagine you have so many terms because you are doing some sort of geo targetting.
When I extensively use geo targetting for a given campaign I typically group words into "baskets". So, if I was doing 200 combinations of the keywords "*Location* Blue Widgets" (location being the term that changes, creating the 200 combinations) I assign that one basket a single referral ID.
I think this is a good way to minimize the amount of tracking IDs you need to generate which will still allow you to see how keywords as a whole convert.
Hope that helps!