After reading the various posts I think you are trying to do too much. Its one thing to track your positions using software. When it comes to reporting for income taxes use the tax forms provided by your brokerage account.
If you look at my profile you will see I'm a retired IRS Revenue Agent. My job was to audit tax returns. One of the things we would review during an exam is if there was a wash on a loss. Remember the IRS and your state tax authority gets copies of all information returns. We will check those information returns to the return. Its when there is a difference then we ask questions to explain. Long story short is to use the tax forms provided by your brokerage account to prepare your return. If the brokerage account is wrong contact then and work it out to get a corrected tax form.
As for taxable and non taxable accounts a friend gave me some advise on how to treat the two accounts. Think of two buckets. One is vinegar and one is oil. The two do not mix.
