Yep,
Start with your list of favorites. Have those in the right quality and fully prepped and analyzed in your system. Make a playlist system that works for you and fill them with the appropriate tracks.
I had a big collection too (slightly smaller than yours) and I am currently starting COMPLETELY fresh. I intend to have between 1200-2000 tracks that make my core collection. The rest I will save as a request system on a separate hard disk.
That way it will fit on a memory stick for playing out in CDJ environments, on my iPad (with my iDJ Pro) and on my MacBook Pro with SSD.
Greetinx.