Make spacers?
I have a box under the bandsaw with loads of custom made spacers in it
Nah, I just have some bits of pipe insulating foam, rubber strapping and other such odds n ends. (this allows a bit of automatic alignment/twist etc)
Your set up is more of a precision job by the look of it. Mine was quick, dirty use it outdoors collapsible version just to get some slo mo vid of flight arrows. Not used it since, but it showed what I needed to know and it may get some use in the future.
I don't think the set up is hyper critical, it's just that you obviously aren't happy with how it's lining up at the moment. I expect you'll soon get a handle on cause and effect once you start playing with it.
Yes it looks like you should raise the bow. This will of course make it look like it will hit where you have seen the arrows are actually going.
You'll need to adjust the chrono position up a tad to match persumably.
Keep us posted
Del