Basically, here are the changes: When Joe's Garage Act I was released on CD in 1987 (the same year the Box Set edition was released on vinyl), it put in the same package as Joe's Garage Acts II & III. The track "Wet T-Shirt Nite" was changed to "Fembot in a Wet T-Shirt", "Toad-O Line" was changed to "On The Bus", and the Central Scrutinizer's dialogue from the end of "Lucille has Messed My Mind Up" was separated into its own track, entitled "Scrutinizer Postlude." I don't know about the remastered vinyl box set that came out the same year, but I assume it had the original names. The only thing close to an explanation I've ever heard for any of these changes is the "Fembot in a Wet T-Shirt" change. I've looked it up, and as far as I can tell it was the subject of a discussion that took place in Frank Zappa's "Society Pages" fanzine, issue #3 (which was published in 1991):

Rob Samler: "What is a Fembot in a wet t-shirt?"
Frank Zappa: "Do you remember the Six Million Dollar Man...?"
Rob Samler: "Uh-huh. sure."
Frank Zappa: "...there was an episode where they were being attacked by fembots...these 'Female Robots"...[if] she enters a wet T-shirt contest, what happens?"
Den Simms: "Sparks fly."
Rob Samler: "So, why did you change the title on the CD?"
Frank Zappa: "Why, what does it say on the CD?"

And that's all. I don't actually have the magazine, but I've heard about the discussion from here, and this has information about the publication, and here's an eBay listing for the issue. So that's basically all I know.