Applecare extends the warranty from one year to three. If they are going to repair the superdrive, Applecare will make no difference. Its already under warranty until August.
I would guess that they will tell you if they find evidence that your DIY repair has caused the drive failure, you will have to pay for it. If not it should be covered.
If you had any screws leftover or anything, its best to consult the engineer before (s)he even touches it. If (s)he says a missing screw is evidence that the fault is yours, take it elsewhere. If (s)he says only a torn ribbon cable or a foreign object or something could have damaged the drive, then you will be OK. Unless you tore any cables or left a screwdriver in there.....
