Thank you everyone for your replies. They have been helpful . I spent a large chunk of my day on the phone with TD Ameritrade and with Vanguard to gain online access to the accounts that they hold for the FA and find out the following information:
I can remove the FA from the accounts. TD will allow me 30 days to name a new advisor and if one isn’t chosen, the accounts will be transferred as new accounts in kind to the retail side of TD rather than the institutional side. After the transfer, I could only hold or sell the DFA funds. TD would charge $9.99 for any trade of the iShares (12 funds across the three accounts) or Vanguard ETFs (6 funds across the three accounts) and $49.99 for any trade of the DFA funds (8 funds in IRA, 8 funds in Roth and 5 funds in taxable). Since there are so many funds in three accounts (which would all be considered separate trades), these charges could cost a bit down the road.
Vanguard confirmed that they can accept all of the ETFs and DFA funds but I could again only hold or sell the DFA funds. Vanguard would charge $7 each for the first 25 ETF trades per year made online and $20 for each trade of the DFA funds. Still a pretty penny.
Alternatively, Vanguard suggested that at least as to the IRA and Roth IRA, I could liquidate the accounts and then have them transferred. TD Ameritrade confirmed that the arrangement with the FA includes all trading costs and that if I liquidated the funds and then transferred them to another institution while it was still on the institutional side of TD, there would be no trade charges. This would eliminate additional charges for these two accounts.
I could also do the same with the taxable account or I could liquidate some, transfer some and try to limit the tax hit. The taxable account is only about 12-13% ($36,000) of the total and according to the current online records has a short term loss of $2760 and a long term gain of $8,820. So I guess the tax hit would not be as bad as I feared. I haven’t prepared my taxes for this year but last year I barely stayed within the 15% bracket (head of household, high mortgage interest, property taxes, college credit for son, etc.). I raised my 401(k) contribution last year but am not sure if I crossed over to the 25% bracket or not. These capital gains would probably push me over, however.
Finally, TD charges a $75 per account to transfer if the other institutions forms are used and the other institution requests the transfer. If TD forms are used and the request is made by me, there is no transfer charge.
So, I would really appreciate any advice as to the best course of action to take with this information. If the funds are okay as they are and ok to stay this way for awhile, then maybe it doesn’t matter or if only a few funds were sold at a time, the expense would not be that overwhelmingly. Or would it be better to just get out of them now and start fresh? I am not sure if there are only holding periods which would incur fees.