Hi Sonorus...I'd be cautious about deleting individual files on the computer, as it may throw off the Tascam's indexing, which allows you to Undo an action.
As far as deleting individual takes, I generally replay a take that I don't like until I get it where I want it. If it's just a section of an overall good take, I'll punch in, play that part, then punch out, as it's easier than doing the whole take again.
I leave previous takes intact until I've made a mix that I'm pleased with, and then one of the last steps I do is select Delete Unused from the Song menu. This will delete the previous takes, and reduce the file size of the song. Do be aware that once you've deleted any unused takes, you won't have the safety net that Undo provides, so be sure you're satisfied before you delete them.
Hope this helps!