That may be more doable, and should still give long run times (probably well over 30 min). Take a look at BrianG's hyper, it uses two 2s packs I believe, that may give ya some idea of how much room you will have.
The 2s packs I used were 2s2p, so 4 stacked cells per side. 3s1p per side should be thinner.
But, to get the clearance for the shell with 4 stacked cells, I had to raise the body mounting a bit. If you don't mind a sloppy looking setup, you could just velcro the packs to the mudguards (I use actual trays) to gain a few mm's.
Some small capacity packs will fit the bill as well. I ran my 2 3S 2200mAh packs in a Ofna MBX with a Hacker C50-13L/BK 3695 combo. Ran for 23 minutes on grass.