Problem 1
Using Asp.Net and an ODBC connection doesn't seem to work. We can't even open a connection with QB up and running on the server console.

Try looking at: ASP page hangs when trying to open connection (ADO and classic ASP) and ASP.NET vs Classic ASP 

Problem 2
Unattended mode does not work. We need to have QuickBooks running and the company file open using the admin user. Your post on fixing the unattended mode is for QB2008, and we're using QB2006. Following the steps there did not fix our problem. And ideas?

The workaround shown at: After upgrading to QuickBooks 2006 or 2007, QODBC "auto-login" unattended mode no longer works? applies to QuickBooks 2006, 2007 and even 2008 before the R5 update.

Problem 3
If we have a 5 user license, and all 5 users are logged into QB, does this prevent QODBC from connecting to the server? Do we need to buy another seat license specifically from QODBC? If we do, that's unacceptable for a piece of software as expensive as yours is.

The normal Windows Service operation is that QuickBooks is on the server and QODBC auto-connects to the company file. If you what to be able to use QuickBooks while the Windows Service is running check the "Launch QuickBooks UI" option.

Problem 4
When we changed the query in the qbcust.asp demo code to us our query, it took over 4 minutes to respond. Here's our query:
SELECT InvoiceLine.RefNumber as InvoiceNum, Customer.FullName, Customer.BillAddressAddr1, Customer.BillAddressAddr2,
     Customer.BillAddressAddr3, Customer.BillAddressAddr4, Customer.BillAddressCity, Customer.BillAddressState,
     Customer.BillAddressPostalCode, Customer.BillAddressCountry, Customer.EMail, Customer.Phone
FROM InvoiceLine
INNER JOIN Customer ON Customer.ListID = InvoiceLine.CustomerRefListID
WHERE InvoiceLine.CustomFieldInvoiceLineTEST = 'SomeString'

This SELECT statement is a little better:

SELECT InvoiceLine.RefNumber as InvoiceNum, Customer.FullName, Customer.BillAddressAddr1, Customer.BillAddressAddr2,
     Customer.BillAddressAddr3, Customer.BillAddressAddr4, Customer.BillAddressCity, Customer.BillAddressState,
     Customer.BillAddressPostalCode, Customer.BillAddressCountry, Customer.EMail, Customer.Phone
FROM InvoiceLine, Customer
WHERE InvoiceLine.CustomerRefListID = Customer.ListID
AND InvoiceLine.CustomFieldInvoiceLineTEST = 'SomeString'

however QODBC will have to scan the whole InvoiceLine table because the InvoiceLine.CustomFieldInvoiceLineTEST column is not indexed. So you really need to limit the scan to more revelant data, like the last two months like this:

SELECT InvoiceLine.RefNumber as InvoiceNum, Customer.FullName, Customer.BillAddressAddr1, Customer.BillAddressAddr2,
     Customer.BillAddressAddr3, Customer.BillAddressAddr4, Customer.BillAddressCity, Customer.BillAddressState,
     Customer.BillAddressPostalCode, Customer.BillAddressCountry, Customer.EMail, Customer.Phone
FROM InvoiceLine, Customer
WHERE InvoiceLine.CustomerRefListID = Customer.ListID
AND InvoiceLine.TxnDate >= {d'2008-02-01'}
AND InvoiceLine.CustomFieldInvoiceLineTEST = 'SomeString'

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