Checkout configuration change made multiple change

I got a complaint that the checkout process was "Not User Friendly".

So, I started reading and changed out of the Advanced Checkout Workflow. I've tried putting everything back, but it is still all messed up.

I lost my custom category displays (still in backend, just doesn't show)
I get 2 "The Cart is Empty" errors on all category pages. Goes down to 1 error when in checkout.html
I lost my domain name in links, reverts to subdomain of hosting company.
Adds sales tax at all times.

Thanks for your help

Looks like I was impatient.

Custom layouts came back
Empty cart errors stopped
correct domain now.

But, still error with tax.

Here are all the screenshots.

Thanks for your help.

I have noticed that the tax seems to show only when not logged in. (Default?)

If not logged in, the shopping cart seems to ignore any items beyond #1.
It will only show 1 item in cart.

This is the same in FireFox, I.E, and Chrome

In Chrome - the connection to view the shopping cart will not connect. Screenshot attached.

Thank you again.