So WAT limits are only related to 25.121 and no other FAR?
The take-off WAT limit is the maximum weight that meets 25.121(a), (b) and (c), the landing WAT limit meets 25.119 and 25.121(d).
So the gross gradient only needs to be 2.4% at the point the gear is retracted, and not a 2.4% gradient from gear retracted to 400'?
Correct.
Is the net climb gradient for determining obstacle clearance reduced to 0.4% then?
That's not impossible - considering 25.121(c).
My understanding is that at 400', this available climb gradient is used to accelerate the airplane to Vfto.
No, the acceleration (at 400' or greater height) corresponds to the available gradient reduced by the acceleration equivalent of 0.8 % gradient (twins) - see 25.115(c).