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what kind o shape is the v6??? is the 5 speed in good shape?? the waggy 44 is good do you have the waggy springs?? um if you keep the toy tranny and v6 id save the atlas for a later project.
as for axle gears? you should probably go with 5.29's, if you stay with the v6 , if you go with a 302 or sbchevy keep the stock gears and get a 4.7 tcase from marlin
