See my edited post. I already decided to download the stupid thing to see what the building was supposed to be like.
The Tower in the DMG is further described in Sword & Fist, one of the first few 3.0 supplements and still reasonably valid for its Buildings section at the back. According to S&F, the Tower, or Border Tower as they call it, takes 8 months to build, excluding furnishings (which it estimates as another 1-4 thousand GP or so depending on type and quality). 2 thousand GP is the estimated annual maintenance cost. The first floor is about 50 feet wide and long excluding the outer walls (which are about 5 or 10 feet thick), the second floor is about 40 or 45 feet wide and long, excluding the walls which are about 5 feet thick, and the third floor is 40 feet wide and long, with walls about 3-5 feet thick.
However, the square footage and whatnot of the Tower/Border Tower is smaller than the Alchemist's Eyrie, thus why the Cheap Keep in Stronghold Builder's Guidebook is a closer fit to what you're looking for.
I think SGB cuts the building times down by a large amount simply for the sake of adventuring PCs; it mentions speeding things up regardless of realism for the sake of making it easier for PCs to get their construction projects finished. Though it really cuts down the build times a huge, absurd amount, I think. So you might go with something more like Sword & Fist's build times. Ten or eleven months would probably be the S&F equivalent for a building of the Cheap Keep's scale.
Actually, checking the sidebar in the first chapter, it says that the SGB's build times assume you're using magic to expedite the process as much as possible. It mentions how real castles and suchlike took years to build. So depending on your players' resources, you may want to use one build time or another.
The services of a Maug should not seriously affect the build times or costs. That's 1 strong, tireless worker, who probably can't haul everything by itself and can't handle every construction task by itself, probably. It may reduce the time by 10% at most I'd guess, same as spending more money on extra laborers.
Surrounding terrain and whatnot will also affect build times and costs. Building on a field not too far from the nearest quarry or the like and not in a hard-to-reach place would be best, while tougher positions would take more time and money to get the building materials to.
The SGB has details on site-based build cost modifiers, which are small percentages. Different climates and locales will affect how difficult it is to build there, and different sizes of towns nearby determines how many workers you can get, and so on and so forth.
My copy is out on loan right now, though.
