Going through your points one at a time, in the order you mentioned them (I'll post a re-code later).
1) Right clicking on the channel should've given you a Blacklist option along with the rest of your channel right click options. I have found the problem with it defaulting to asking for nicks, and resolved it. The option was added in case you wanted to add someone to the black list that was no longer in the channel (eg: someone joining, spamming the channel with an advertisement, then leaving)
2) The greyed out options have been resolved, and were due to the same problem that was causing the problem solved in #1.
3) I noticed this also, and while I can see what is causing it, I'm going to need a bit more time to figure out a proper resolution for it.
4) Reference answer #1 for my reasoning on having the options available in the status & channel menus. Removing the option is easily enough done if you really don't want it.
5) The kick counter is stored in the hash file, and tracks the number of times the particular nick was kicked, rather than the total number of kicks. When you said about a kick counter, I didn't realize that you only wanted it to count when you kicked someone. Adding that condition is easy.
6) Removal of the aliases is possible, but would increase the amount of code significantly since the code that is in each alias would have to be replicated for each part of the code where the alias is currently being called. I do not recommend this, as it would mean haing to make 5 changes to the code, rather than 1 change in the alias.