If you put in the screws with the rubber washers on them you should be OK, thats the proper fastner. My suggestion would be to make sure the new flashing you installed on the transition from the metal to the shingle roof extends at least 3" up and under from where the water valley is in a 3-tab shingle. Form a straight break in the metal flashing and turn it out at least 12" onto the metal roof. At Lowe's or Home Depot in the roofing section, by the metal roofing panels you will find foam "closures" install them in every flute section along the bottom of your new flashing to prevent water, debris, and wasps from getting up and under your flashing. You can buy "trim coil" at the big box stores that is 24" wide and use this for your flashing material. When you screw into your metal panels make sure the screws are straight and you screw next to the ribs and not into the ribs, you want the washer to have direct contact with the flat pan.