Somewhere along the way something didn’t go right…normally the ideal solution is to reverse what was done and to go back to the point everything was working 100%. Don’t feel bad because sometimes this happens…in fact I had to recode a lot of things for my latest theme because I was trying something new but didn’t quite work out.
Anyway, you have a few options, and one is to try another theme and see if you run into the same issues, and if it does, then you know it’s either a third party plugin being used or something missed or done in error with content. However, if another theme displays everything correctly (although in a different style), then it could be related to the theme.
Your other option is to start from the beginning, rebuild the site on a development location, and as you go along with adding content, plugins, etc., check the front of the site and when it looks good, then move on to the next step, and so on. This way if something goes wrong right after you add something, then you know it’s related to what was just done and easier to track down and find a fix.
Sometimes we just have to or that it’s just better to start over…and I’ve done that many times.
As a side note, if there is a theme tutorial that you feel is missing on how to use or setup a feature, please let me know and I will look into the possibility of adding it to the theme setup videos. Basically anything that will help everyone out more.