You created inventory assemblies, but you never entered a BOM, edit the assembly item and insure the listing area of parts to be used is blank - is it?

Have you been selling the assembly item? 

After 17 years that file is going to be hard to fix depending on exactly what is wrong, and fixing it may impact on previous IRS returns, which might require amended returns.

If it was me I would continue as you have been this year, and use the rest of this year to set up a new company file.

As far as inventory and making your product, I would use the periodic inventory method and not mess with QB inventory at all.  QB inventory does not deal with scrap or left overs at all in an assembly item

Use a service item to sell the various models of product you make

Using periodic inventory will require you to keep a listing outside of QB of product and model assembled that are on hand, but once you get a system set up it should be ok

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There are two ways to do periodic inventory, choose one and stick with it, you can not mix and match

1. (my preference) Create an asset account called purchases and post all purchases of item for resale to that account.  Periodically, weekly, monthly, etc value the inventory on hand, subtract that value from the amount shown in the purchases account and do a journal entry for the answer to the subtraction
debit COGS for that value
credit purchases for that value

OR

2.  Post all purchases to COGS.  Periodically, but at least at the end of the year, you value the inventory on hand and do a journal entry.
debit the asset purchases account for that value
credit COGS for that value

Print the P&L
then reverse the journal entry
debit COGS for that same value
credit the asset purchases account for that value

This last journal entry, moves the value of what was on hand at the end of year back to COGS so the cost will be counted against the new year sales.