Getting no errors with IR is going to be tough. The problem is if it misses one blink, it gets all shifted, then your screwed. Sending 2 at a time will also be hard, as the arduino an't do parallel processing.
I would recommend a different protocol. IR is not great for lots of info. serial is super easy if you don't need wireless, if you do, go with bluetooth, such as 2 blueSMIRFs. you will have to set one up as a master, but then it is just like serial communication.
Do some googling, but I think IR is not going to work out with whole messages. 1 or 2 numbers, sure, but a whole sentence or something is just not going to work out well.
the one thing to try would be to send the message 2 or 3 times, and compare to see if they are the same. if yes, chances are it is right, but if different, you could request a resend.
you might also want to slow it down if you can, and use longer pulses and pauses, that will give it more time to register, meaning it should be more accurate.
good luck!