I totally agree with Hammer. As far as blocks go, the GT block is cast iron. The Cobra's is aluminum. Also, the intake does have coolant flowing through it. I found that out the hard way when mine cracked while racing another GT. Not to worry though. Ford has a recall on it. Apparently the intake was cast with sidewalls that were too thin. The recall was only for 96-97's, so anything 98 or above will be ok. As far as expense, the 4.6 will be much more if something ever breaks internally, but as for mods it is not that much higher than the 5.0. Hope this helps.
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