Sell the shares in the order you like, but keep good records. Use a spreadsheet, but also use manual methods as further verification.
For example, I always print the confirmation records and staple the SELL confirmation to the one or more BUY confirmations it relates to and file these with this year's tax return. If BUYS are split over multiple sells, then photocopy the BUY confirmation. Staple one copy to the SELL confirmation, manually indicating the amount sold and file with this years tax records and keep the other copy showing the unsold quantity for your subsequent years' records.
You don't have to do this, but if you DON'T want to use FIFO, your records need be good in case audited. I find using a spreadsheet and a manual system like I described makes it pretty clear what batch or parts of a batch have been sold.
