Well, I know how to do FIFO in BizTalk – not specific to HL7.
You might want to look at this sample
http://www.biztalkgurus.com/Labs/Sequentail-Message-Convoy-Flat-File.html
To get a true FIFO you need to have either control of your input to make sure they send messages in order or receive messages via a FIFO friendly adapter like queues.