Is there a way of telling which factory has which number?
I have had an alert telling me that 2 objects are missing construction robots on Factory Floor 12 for a while now and I can't figure out which one of my factory buildings it is.
When I click the alert it sends the map to a place where there aren't any factories, near coordinates (0.0, 0.0)

Unfortunately no, Factorissimo provides no help there. However, you can find your factory building using some tricks:

Factory Floor 12 means it's the 12th (or 112th, or 212th) factory building you've created. A construction bot alert means there's a roboport inside that factory building, so that may also narrow it down some. To find out the number of a building, just cause an alert inside it, for example place a blueprint in roboport range without a bot, and see which surface you get.

I may add a method to find factory buildings by alerts later.

This would be a really helpful addition. I've got at least 20 factories, and 3 of them are showing various alerts, right now. Gotta go to each one to find out which the problems are in. :(

Would it be feasible to have a numeric overlay (eg. Nixie Tubes) which shows the floor number? In theory, it should be cheap in terms of UPS, given that the floor number doesn't change. I think the the most awesome thing to do would be to have the factory's serial number replace the big '01'/'02'/'03' painted on the outside, and/or the big number on the floor.

Looking at the code, it should be relatively straight forward to update the number on the floor, given that it's created by replacing one tile at a time. It might be easiest to reach for one of the mods that generates a blueprint that contains text written using a pattern of tiles, but it should be relatively straight forward to achieve. You would need to have a mosaic for each character you want to draw (all of the numerals, and perhaps a dash), instead of drawing one mosaic in the exact centre of the factory floor, you would draw a set of mosaics (one for each number). I suggest a dash, as it would make it feasible to have "Factory Floor 12" which has "12" and "1-12" (or perhaps "12-1") 16 chunks distant from each other, but also make it clear that they're somewhat related.

Sorry for the necro but is there any waything new that allow us to locate factories by floor number? I have 100+ and can't find one for the life of me.

Nothing is really planned, but if you don't mind cheating, you could simply teleport to the surface called "Factory floor X", where X is the number in your alert. The center of the first factory on that floor is at coordinates (0,0), the next factory is at (512,0) and so on.

Could you please give me the total command? Semms like I am doing something wrong.
I imagine it would be something like:
/c game.player.teleport({0,0},factory_floor_14)

Here's the documentation.

The correct command would be

/c game.player.teleport({0,0},"Factory floor 14")

Thank you very much!