1. If the high end is your problem, it has to do with the tweeter, and that will need some break-in before that sounds its best.

2. The bass drivers need some exercise to loosen up their suspension, then you should gain a bit more low end extension.

3. How did you dampen and brace the speakers, maybe try to remove a bit of damping to see if that clears up the midrange.

I have build many gainclones, and they all sound great, but again they need some break-in.
Do you know the value of the input capacitor on the amp, is it 47uF ?
If it is you should be alright.

My suggestion is this:
wire one speaker in reverse phase, and put them pretty close together, face to face, cover them with a blanket to minimize the sound comming from them.
Then play pink noise or just some rock music through them for a day or so, then they should start opening up.
You should play it pretty loud so you can see the bassdriver moving, but not bottoming out.