So I read this post at Classic DOS Games and started wondering wondering exactly what kind of Keen stuff there was on the floppy image. To my surprise, it turns out that they hadn't used a clean disk to produce the sample disk this disk image comes from at least. In fact, they had used a disk they used during the development of Keen and then just emptied it and added their sample games.
After doing a quick check I noticed there were a bunch of overwritten file indexes which made references to different .CK1 and .CK2 files. Luckily, the method they had used to erase the files from this disk didn't actually destroy the data, but just render it inaccessible by normal means.
Most of the Keen 2 data had been overwritten by the sample games, but to my surprise most of the Keen 1 data was still intact and after scratching together the deleted files I managed to get almost a fully running game. Only EGAHEAD.CK1, EGALATCH.CK1, EGASPRIT.CK1, HELPTEXT.CK1 and LEVEL01.CK1 had been completely erased (well LEVEL01.CK1 had about 50% of it's data there but I didn't bother combining it with the finalized one), so I took these missing files from version 1.0 of the game.
Now I was a bit disappointed that I didn't get the graphics files together (usually graphics are what's most interesting in development versions of games), but it seems the other game files were actually quite different at this point as well. I don't know at exactly which stage the game is in this build but it at least looks pretty close to final with a bunch of minor level design differences in quite many levels.
The story section is no doubt the most interesting difference, you actually get a scene where a Vorticon comes to your ship and takes the vital parts and then leaves (explaining why these tiles without and with the parts exist in the final game).
Other points of interest is the lack of the GOD cheat and the fact that you can't complete the game.
You'd better believe it!
P.S. If someone feels like taking another look at the disk image, please do! If by any chance the graphics files or any other file I didn't recover could be recovered that would be just totally awesome.
EDIT: Now includes original file modify dates and some of the corrupt files.
EDIT2: Now also includes almost completely corrupt Keen 2 files.
EDIT3: Fixed KEEN1.EXE and LEVEL90.CK1
This is such a great discovery!
But if true, and I have no reason to doubt it, this is an amazing discovery!! 
Great work. Another rarity from the past, but the best one so far. I'll write more once I get to see it.
