I've only vaguely been following along, but recently I had some problems building libsodium on a RHEL5.4 system due to no long-long support.
I'm not at work so don't have access to the build script I use, however from memory I set CPPFLAGS to contain 'Wno-long-long' and the compile issue was silenced and make check worked as expected. I'm not sure if this is a possible solution to your problem but I have not seen any mention of the Wno-long-long and libsodium combination. I thought I'd mention it on the mailing list for posterity.
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