Cooling problem on a s/c 93' Cobra

Ever since I had to replace the lower intake gasket I have an air pocket that I can't get out. The car is supercharged and I want to make sure that it is an air pocket rather than a head gasket. I don't want to go through the time of a head gasket replacement and have the same problem when I am done. There is no oil in the antifreeze, no antifreeze in the oil and no smoke from the exhaust which leads me to thinking that it is an air pocket. The temp will spike then come down a bit and then spike again after a few miles. It doesn't seem to be affected when under boost. I recently had to run it without the blower belt and temp does the same thing when I run it through the gears without the blower. Eventually it will push water out the overflow and when it cools the radiator will be half empty. Any help or suggestions will be greatly appreciated.
 
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Did the radiator get lowered at any time?

The overflow needs to be the high point in the system. This is more common of a problem on taller 351w conversions, but that is all I can think of now, assuming no failed parts.

Check that the rubber mounting tabs are on the bottom of the radiator.

good luck
jason