You will need to decide what shipping rule will take precedence, then for the other shipping rules you can check on the opposite of the conditions for the main rule.
So if you wanted the first rule in your scenario to take precedence you would need to alter the other two rules like this:
item 2 qty = 1 shipping is $6.50
In this rule you would need to add the opposite condition of the first rule, so in here you would add a condition that says 'and if item 1 or item 3 does not exist in the cart'. You would do the same in third rule, you would need to add a condition to make sure that items 1 and 3 are not in the cart.
The charge rules are very flexible and you can account for many situations, you just need to determine in advance how exactly you would like the charges to occur then based on this configure them to fit your scenario.
