Total is way off at checkout

What in the world is going on?

Subtotal is correct. Confused on what the blank line item is and how we got the Total to the huge number it displays.

1. We need loads more info, try filling in the posting tips
2. What modules do you have installed, have you installed, uninstalled or reinstalled anything recently
3. read this thread http://www.zen-cart.com/showthread.php?186505-My-order-total-is-way-off-800-to-3k any of that seem familiar to you

I'm using 1.3.9h and have added password protected pages and multiple pricing levels. (We're currently not using these features) When it was first done I added a test item and it worked properly, I was able to use my credit card and it posted through etc.

Now the totals are crazy. Still don't know what that blank line item below shipping cost and total.
Here is another example:

$115.00 Sub-Total:
$17.97 United Parcel Service (1 x 6.00lbs) (Ground):
$7.48:
$2,268.95

1. You said "it did work fine" and now today you're saying it doesn't. So, "when" was it "fine", and "when" did it suddenly break? What changed in the meantime?
2. Who has access to your site?
3. What's different between your site and original Zen Cart code? The detailed list will be a helpful tool in your diagnosis: http://www.zen-cart.com/wiki/index.php/Troubleshoot_-_Diagnosing_Obscure_Issues
4. How long has that "blank line" been showing? It's probably that you're missing a tax description in your Tax Rates settings. Or maybe it's from an order-total module you've added that's malfunctioning and also the cause of the wrong calculations?

Not quite sure when things went wrong. Besides myself two other people have access to the site. One of them is doing nothing other than adding and editing products and categories, the other is on these forums and is a trusted person with tons of experience. I was recently having issues with attributes so I asked for help and provided access for the trouble-shooting process.

I'm not quite sure how long the line has been showing. The last time I tested the checkout was a few months ago.

Looks like there are a number of items in my debug log. What's my next step?

Next step? see points 3 and 4 from my prior post.

There is likely a great deal of differences in the files as I'm using a theme with a couple of add-ons.

As for order total modules, I haven't installed anything like this.

How would I find a missing a tax description in my Tax Rates settings? I only have one tax class but there are 41769 tax rates which were imported from a previous shopping cart.

Made some progress on narrowing down the issue. I went through the debug log, the three errors it posts are:
/includes/languages/english/meta_tags.php on line 14
/includes/modules/sideboxes/manufacturers.php on line 121
/includes/templates/theme457/sideboxes/tpl_categories.php on line 20

I doubt any of these issue could be the culprit.

One other thing I tried was making the items in question non-taxable which got rid of the blank line item issue as well as the incorrect inflated total issue, so it's clearly a tax problem.

The tax database is huge with 41,769 tax rates and was imported from a magento cart (ported). What can I do to fix this? Will this involve deleting these tax rates or is there a simpler solution?

Could you provide a couple screen shots of the first page when browsing the two tables:
tax_class
tax_rates

Here they are:

Do ANY of those tax rates ACTUALLY apply to things YOU are registered to collect and remit tax for? Or are they just a huge list of POSSIBLE tax rates that one MIGHT use, and were forced upon you by a default Magento install?

ie: do you know what each of those rates is there for, and do each of them actually apply to your business?
If not, why not wipe them out and set up just the rates that YOU actually need?

If they ARE all required by your store, then you'll need to rework how they're used, and set up all the required geo_zones records to match each of the tax_zones you've got in that table. Right now you're likely getting it applying all taxes on top of each other regardless of zone because you probably don't actually have matching geo-zones for any of them. Just a hunch.

These are being forced on us, there was a Avalara module integrated into the old magento cart that dumped all this info into the current database when it was migrated over.

I would be inclined to truncate the tax-rates table, and do any other resets needed to undo whatever the Avalara stuff added, and then if you still intend to use an Avalara tool, add that fresh after you've got things working properly without it.

What's the easiest way to get rid of that data without causing any other problems?

Who do you really need a Tax Rate for?