The 4 for the battery box as mentioned, are probably best left in my opinion. The 2 together near the centre are for my extra toplate upright. The three in a line below that are fuel tank mount holes for the mugen mst-1 tank or the stock cen tank. And the single hole at the bottom is JTs position for the exhaust hanger (Idont use it, its way out...). We need the fuel tank holes tho, and if this is just a prototype... could we leave the others in too for now?
I like the idea of the chassis edges being bent up tho, it would just about cure all flex issues very simply. Thatd mean much less stress on other parts... sounds good to me - do you have facilities to bend up 1/2" or so extra on each side?