Using only R1 reads, how do I really start?

I’d like to analyze just the R1 reads in my MiSeq data. I know it basically should work using the 454 SOP, but how I should start with the big bunch of separate fastq files I have. Mothur doesn’t handle several files in one go, and if I merge the files I lose the information on which sequences came from which sample.

I know there are previous threads on the topic, but I don’t see the question actually really answered anywhere (other than runnig etc. one by one on all the files).