To solve the issue with the categories list, copy across these lines from the Default qa-styles.css to the qa-styles.css file for you custom theme:
.qa-nav-cat-list ...
.qa-nav-cat-item ...
.qa-nav-cat-link ...
.qa-nav-cat-selected,.qa-nav-cat-selected:hover ...
Some other key changes in qa-styles.css you need to copy across:
.qa-sidepanel ...
* html .qa-sidepanel ...
.qa-sidebar ...
.qa-feed ...
.qa-feed-link ...
.qa-nav-main-item,.qa-nav-main-item-opp ...
.qa-nav-main-item ...
.qa-nav-main-item-opp ...
.qa-q-view-hidden ...
.qa-q-view-hidden .qa-voting ...
.qa-q-view-hidden .qa-q-view-content ...
.qa-q-view-hidden .qa-q-view-meta ...
.qa-q-view-hidden .qa-q-view-meta .qa-user-link ...
.qa-q-view-hidden .qa-category-link ...
.qa-q-view-hidden .qa-tag-link ...
.qa-nav-footer-item ...
.qa-category-link ...
There are also some less crucial changes - you can see the full list by comparing the Default qa-styles.css file between version 1.0.1 and 1.2.