So, in addition to what I listed above, you reckon the following measures could help mitigate such imperfections. First of all, for the letters, you'd need to make certain that they all get as close to a uniform height as possible. making molds and casting the letters could help get that uniformity without having to spend more time making them by han, though it does mean more up-front effort if some new symbol is required. The other area, the pressure exerted during the printing could be helped by including a spring-loaded mechanism or similar to ensure that the pressure is always the same, and is not dependent on the operator.
Another option could be to have the plate be applied twice rather than once to increase the chances of one of the two applications being 'correct', though you would have to ensure the paper does not move at all between applications.
edit: @windstruck, you could continue with that, yes, though you're close to done with preparing the paper.