urahara sealed the hougoukyou right after he created it. aizen says so, and thats why he didn't know anything about it. aizen was the one who expierimented with it. Aizen even said that uruhara tried to destroy the hougokou immediately after its creation, because he feared that it was dangerous. And because he could not destroy it, he put it within rukia's untraceable gigai, so it could be never found again.
And YOU made up some wild story with no backup at all, and there are no "ex-vaizards" they tell ichigo its impossible to return to normal,EVER. If you read the story well enough you'll notice that.
And i never said flawless, i said it had no plotholes, no loops etc, he backed up his ideas with stuff that corresponds with facts from the story. (although they weren't explained all that well.)
The only "fact" you have, is the fact that shinji and co already learned how to control their hollows, which is obvious. And Shinji has not been show to have any relation to urahara, besides knowing that he existed in soul society, which should be basic knowlegde for any shinigami in the gotei 13.
And yamamoto doesn't want urahara kisuke dead, he asked for his help in the last chapters =S Yamamoto asked urahara to create a door to get to hueco mondo that captains can pass through. If he could ask him for help i'm sure they could have killed him long ago.
And the reason he was exiled WAS because he created an "untraceable gigai"
and in exact words from the manga, "He developed a special matierial that did not contain spiritual matter, and becaus he created an untraceable gigai using that special substance, he was exiled." the main explanation is in chapter 175
"Knowing is not enough, we must apply.
Willing is not enough, we must do."
- Bruce lee