Well, I didn't check peteandwally's quest file, but it sounds just like what I did. Since I'm using version 2.10, I used direct warps to warp you to the screen where the NPC talks. On this screen, I have layer 5 set as a screen that has the black box which, BTW, is one-and-a-half tiles high with the half-tile being above the full tile. Then, on the same screen with the black box, I have flag 16 set to all of the box with the secret set to a blank combo (I believe combo 49 is the standard blank combo for Classic).
That's it other than making sure "Enemies->Secret" is set for guy rooms using the screen that have a Shop room type (or anywhere it's supposed to disappear).