The trick is to line up the marks BEFORE you take the engine apart.
Now, you have a miss timed mess, not to worry, the Chiltons book is full of crap
on how the cam timing is supposed to be. The real way is crank mark up, cam
dowel pin down, ya I know the cam backplate has a mark in it, but this works for
firing #1 cylinder, otherwise you need to time it to #4 cylinder, so if you put the
wires all back where they were, and you are sure you have the crank/cam timing
set as you said, both marks up, you need to swap plug wires to opposite sides,
#1 to #4 and #2 to #3, this should get you started, but remember the timing
will need to be done from #4 now, and the smog guy will scratch his head when
he can't find the timing mark on the crank pully
Good Luck
Wild