The 99+ blocks are better than previous years. The 01-04 blocks are considered the best by design, even compared to a supercoupe block.
Any transmisson that will bolt up to a 5.0 will bolt up to a V6. This is with the proper flywheel, or flexplate, etc...
You are going to have to make all kinds of power in order to be worried about the block though. Only time there is trouble is when other parts give up.