Not sure how thick the walls are, or  any core shift on those blocks.   They are heavy!!   Over at the HAMB site they have a forum specifically for the Lincoln Y's.   I'm  not sure if the stroke is different than a 332,  but 302 and 332's had a dropped forged crank.   Guys are stroking them and getting close to 426 cubes out of 368 blocks.   All it takes is MONEY.    

Theoretically there is a lot you could do to a 279.... but cost effectiveness would be questionable.  Egge machine can probably provide a piston.  Most shops could rebuild the heads and install conventional (non sodium filled) valves.. The cam can be reground to a slightly hotter profile..A Lincoln 317 4bbl intake could be sourced but In the end maybe you gain 20 horsepower for all the expense and effort.. Any member of the Lincoln Y Block family will be the same physical size and have same bellhousing bolt pattern and could be substituted for the 279... The 279 is the least desirable version of the engine family... If you keep the 279, disassemble it,  see if you can reuse the pistons,  do the heads with modern valves, rings bearings and a reground cam and call it good..

Just to clarify.. the 279" was a  Truck engine period, it was never used in Lincolns.
 


Paul