If your parameters will really cause a difference of dimensions, it will only be possible to do this with variable-size signals instead of changing parameters while running the simulation. At Model Update (Initialization) blocks like a Gain will get fixed dimensions. It is not possible to change these dimensions during a simulation.
Instead you need to work with variable-size signals. There is quite a bit of good documentation about this and you may want to start reading here if this is new to you: http://www.mathworks.com/help/simulink/ug/variable-size-signal-basics.html
You could use a Multiply block instead of the Gain block and then you can have a Switch that switches between different "parameter" values at a predefined time (comparison with a Clock block). You could also program the logic of changing values and sizes in a MATLAB Function block.
