I don't know about the dodge V6, but I know on a big block chevy, the chain timing set can go on about 6 different ways, and the belt timing set (that we use) is very easy to install mis-aligned.

You made sure you put it on right?

 

#1 and #4 are 180 out.

How are you determining "compression stroke?" Both will be at TDC at the same time but only the one to fire (power stroke) will have BOTH valves closed.

If you moved the distributor at all the fuel sync needs to be reset.

I know what the "dots" are but am not positive on the lines. If you rotate the engine over two full revolutions do the dots come back into line?