You should be OK using the shorter ones on the long side. I encountered the same thing last summer building the rear wheel for my DH bike. I wanted to stay one length of spokes so that I could get the economics of a 50-pack.
Just be aware that when you start lacing, it may feel like the nipples are just barely catching threads on you 'long' side. Don't panic; it should settle in and you should start catching plenty as you work around and start running things down more and snugging up.
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Originally Posted by Mark Twain
"Don't argue with stupid people; they will drag you down to their level and then beat you with experience."