The block of the 2.8, 3.1, 3.4, 3.5 and the new "3.9" (which is technically 3.7L but whatever) pushrod 60° V6 are all basically the same, with minor improvements from generation to generation (the older 2.8 and 3.1L engines are 1st gen blocks IIRC, the newer 3100 and 3400 are 2nd gen and the 3500 and 3900 are 3rd gen, although I'm not totally certain that the 3500/3900 block is any different from the older 3100 and 3400's, check
www.60degree.com). Likewise the heads were changed and improved in design from generation to generation along side the block. The heads from the new 3900 240HP engine should bolt onto the block, but you'd have to bore out your block of course, and I doubt you could use your old intake manifold, which means you'd have to use the new 3900 intake manifold, which means you'd have to use it's throttle body as well and I'm sure it has electronic throttle control, or figure out a way to mount the older 3400 throttle body on the new 3900 intake manifold. Also the 3900 has variable valve timing, which means it likely wouldnt easily drop into the 3400. Which is sad because it's probably a very nice street grind cam, something along the lines of what most people here would be looking for.
I think the old 3.4 DOHC block is based off the design paramters (IE the stroke and bore spacing) of the 3100 and 3400 blocks, but obviously with changes in the lifter galley and at the front of the block for the cam chains. And likewise with the new 3.6L DOHC, it shares it's bore spacing with the pushrod sixes but I'm pretty sure it's been more thoroughly engineered and refined such that you couldnt really gimp any parts off it.