Couple noob questions I KNOW you guys can answer.

The 289 bored over .040 means the block has been disassembled and machined to "clean" out the cynder bores. It makes the engine itself a little bigger on the bore (something like a 294+/-). It does not effect the internals except for slightly bigger pistons and rings. Now, if it has been machined .040 over, the crank has probably been worked over as well with usually in the .010 range. Again, it shouldn't effect after market changes.
What type of aftermarket changes do yo refer to? Most engined are done at .030 overbore so the .040 makes the cylinder walls pretety thin and suseptible to over heating. Someone else can chime in on that.

I dont think just an .040 overbore would make a 289 prone to overheat. Something like an .060 might, but even then I've heard of many that dont have problems.