Did you calibrate the top monitor? It should work correctly as long as your top screen has a touchscreen and you move the touchcreen connector from the top screen to where the bottom screen usually goes on the mpu.
As for getting an iDeck on the player panel. I did my conversion by removing the entire top part of the player panel and then cutting off the section that is 3/4 of the way to the right that goes across on the top, then an iDeck from a v22/22 or a V32 or V22/32 will fit in the remaining hole nicely. Some people leave the side bumpers on, some leave it off. I left mine on. There's also a rectangular iDeck button panel designed to be a direct replacement for the alpha 1 decks that Bally did in order to upgrade Alpha 1 V32 cabinets to Alpha 2 V32 cabinets. They are more difficult to locate, the last one I saw on ebay was selling for about $600.00.