I'd get the bowler up and running before you do anything crazy. It's not like you can just plug a head from another game in and expect it to work.
Bowling Alley is a coffin style game where a lot of the mechanicals are under the lane. 3-Way is a shuffle alley with all the game logic in the head. Not to mention I think your reasoning is to add two game options to your bowler but one of those on 3-Way is flash. Flash utilizes lit inserts on the lane that are not on the alley in your ball bowler.
There are guys that can do this sort of thing but it would require some serious re-engineering to make it all work. You'd be better to sell your Bowling Alley and put the money toward a later game if multiple games is super important.