I also thought about that but then how would I get the next and back buttons to also correspond with the buttons in the flash movie and the html wrapper as well. Like clicking images on each page?
I was trying to look at the example http://www.lux-manga.jp/manga/15466512efc0c7d932 which is what I want. I can see some jquery in their code and some other things as well. I am just trying to piece it together. Its probably not a job for one, but I am the only IT person here and even though I say it cant be done with our software (in design you have to say no sometimes), I have the time to figure it out and try. They keep on sounding disappointed when I tell them I cant get the same style lightbox as the above example, LOL!
I will try to dig more in their code and find out what I am missing... 
I suppose it wont hurt my process being here in the forums in case someone in the future tries to do the same. Becuase there are seriously no online references for this, haha.
<3