X2. Or If you do, reinforce it heavily. Remember, a steel member's strength comes from it's height (think I beam or C channel). By cutting a notch halfway into the frame, you weaken it by roughly 50%.
Also, consider how the 59 cab will sit on the X frame before you make cuts. Body Mounts? Engine Clearance? Steering/Brake Master Clearance, etc.
What CAD program are you using, and where did you/how did you make the frame profile for the trucks?
A notch in the frame is nto set in stone at this time, just an idea. But yes, it would be reinforced with a triangulated c frame up top above the pumpkin of the rear axle. Probably by using peices of the old explorer frame

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As far as the cab, ill know more when I get it in the garage. Im having a feeling i will have to cut out the 59 floor and firewall and graft in the explorer floor and firewall to compensate for the increase height of the motor and tranny. If you look at the explorer frame, the tranny sits considerably high above the top frame rails. In the factory 59 setup, it barely sits above the rails, so just setting the cab on the modified frame, the tranny and most likely the motor, will hit the floor of the cab before it even mounts.
Speaking of mounts, from my intial eyeballing, the front cab mounts will be explorer spec, the rear cab mounts will be 59 spec. Again, all this is subject to change. Reason I say this is every thread and every picture i have found on the net using explorer parts, the f100 is sub 1956...cabs changed greatly in 57 by becoming wider with intergraded running boards. Because of this, I dont know how the cab will fit exactly until i get a template or the real deal in my hot little hands
As far as cad drawings, i wish I was that talented. I used MS paint and ford body specs for my drawings and just modified the drawings to fit my needs. That way, the wheel placement is roughly in the right spot. And you know, i have started entertaining the idea of increasing the wheelbase on the 59 after all depending on how the stock wheel centerlines feel the wheelwells. this would be a pure cosmetic change only....that and I wouldnt have to shorten the driveshaft
