NO to both...
A TJ top will not fit a YJ due to the windshield frame angle. However, a CJ top will fit a YJ with very little complications. But, the CJ hard tops don't have the modern things a TJ top has, meaning the tinted glass, rear defroster, wiper.
Same goes for the flares...TJ flares are utilized on YJ's with wheel well modifications, but not the other way around. I guess you could if you cut the metal correctly.