Editing Caffe Prototxt input size

So I've been trying to edit a couple of Caffe prototxt files to allow for different image input size and output classes (two output classes).

My two chosen networks are Inception V3 and AlexNet (I've already tested VGG16 and VGG19 successfully).

The AlexNet prototxt I am using is this one, and the Inception V3 prototxt is this one.

So the edited input size on the VGG16/19 prototxts looks like this:

input_dim: 64
input_dim: 1
input_dim: 32
input_dim: 32

... which works perfectly. However I must be missing something as doing this in the AlexNet and InceptionV3 prototxts fails with an error such as

Caused by:
    Layer 'pool5': Input size mismatch. Size of input to
    this layer is different from the expected input size.
    Inputs to this layer:
        from layer 'relu5' (1×1×32 output) 

Now it has been a while since I edited the VGG16 and 19 files, so it's likely I've simply forgotten a step or two! So any help would be appreciated.