To ease weighting vertices, I've come up with the panel visible in the screenshot that you can use directly from the interface to edit the weights of selected vertices. I've also enabled vertex selection in Animation mode (required checking the transformed positions of the vertices against the selection rect, nothing to horrendous) so that you can now edit vertex weights live while the joints are transformed so you can see the effects immediately.
I've also added in the option to draw the weights, hence the strange coloured legs. Whatever joints you have selected, it renders vertices assigned to those joints from red to blue based on how strong the weighting is.
I quite like this character body. Going for a slightly more stylised look than normal seems to look better with low polygon models.
There is also something really satisfying about making a model from scratch using software you have written yourself, I'm finding. I've done a bit of modelling with Milkshape before but seeing the results not just of the effort modelling, but of making the software easy to use as well is very rewarding.