http://www.9mracing.co.uk/html/modules.php?op=modload&name=NinemeisterContent&file=index&req=viewarticle&articleid=9&topic=4&articlename=3.8%20Litre%20Racing%20Engine%20Build
check that out, build up of a 3.8, the pieces that were used and why. I am sure some would argue for other parts but its a nice starting point. Have you called up any of the reputable engine builders that are often mentioned here? I would call Henry Schmidt (supertecperformance.com), Steve Weiner (rennsportsystems.com) and Jerry woods to see what they have to see. I think the weak part in the 993 rods are the bolts but not the rods themselves. You can always bolt 964 rods onto a 993 crank cant you?
Why not just take either 3.6 mill, put in some hotter cams, higher CR pistons, top it off with ITB's and get a nice DTA or Motex ECU and have fun.