In your model, the clcok time is getting multiplied with each element of a vector, that's why "Why" and "Why2" are 2001*2001 vectors.
To get the desired 2001*1 output vector, you need to specify the input as a time varying output.
You can refer to the model configuration in the attached simulink model (demoModel.slx) and resolve your issue using a similar approach.
Before running the model, run the following commands in MATLAB command window:
a = 1 + zeros(2001,1);
t = 0:0.005:10' ;
Use scope to analyze the ouput of the simulation.
The solver settings are as follows (Press CTRL+E to get there):
The Data Import/Export settings are as follows: