I'm sort of doing the same thing, just not nearly as many cards. I'm really only scannnig the cards i'm selling, more that I can provide actual images of the cards reather than using stock photos. I've looked into some business card scanners that over higher res scans, but it'll cost you. I can't justify the cost for me at this time. II have a newer multifunction laser at home with a flatbed scanner. I'm scanning about 8 cards at a time, cutting and cropping with photo software and organizing in a file structure..
example: \Topps 1989 Football\Card# Name Front/Back.jpg.
For my collection, I use Excel. I've either had to create my own or in some cases been lucky enough to download a checklist in XLSX format.