Decent suggestions thus far, I'm especially liking the one when they one-up each-other because I strongly think this should be played as "best in the world vs best in the world" match. It'd get Punk over more that way in my opinion, don't want it as a typical WWE title match, this feud could go much further than that.
It's hard to book it without knowing how long Jericho is going to be back for and what type of gimmick he has. All we know thus far is there's a "she" (Steph likely) and it's a dark sort-of gimmick where phrases like "it'll be the end of the world as you know it" are often said. Presuming it's Steph I'd most likely do this. Jericho carries on his lonely appearances but this time will cut promos. Eventually it leads to the reason why yhe beat down Punk, and who the "she" is. Steph returns and is the women who has been receiving Johnny Ace's texts. She takes control of RAW and is using Jericho as her tool to get the title (where she'll be more protected from getting booted out of power, that way if she gets fired the title comes with her) and Jericho using her as the power he needs to get the title & his rightful place as best in the world.
With Steph in control, you don't see Jericho compete once. You only see cheap-shot attacks & further trolls. EC comes & he wins, again, not competing much at all. Punk is first one out, lasts through all the stars. Jericho comes out and finishes off a very tired & overworked CM Punk. This way Punk's protected from looking weak, and Jericho still looks strong beating Punk clean. As champion Jericho starts to address Punk. They go at it week after week on the mic with let's face it, probably promo-of-the-year material. The match becomes official at WM, best in the world vs best in the world. Perhaps, if Jericho is leaving after WM then it'll be a loser leaves WWE match or something. Each week they compete with randoms and really try to impress each-other for that best in the world phrase.
At WM odds are stacked against Punk as Steph and Ace running RAW keep trying to perhaps get him injured or something. Make it so Punk is the REAL underdog so when he leaves WM as champion it's epic. If Jericho is staying until Summerslam, I'd make Jericho retain at WM with HHH coming down and costing Punk the match turning mega-heel. Now you have HHH, Steph, Ace and Jericho running RAW as the conspiracy all along, perhaps Nash returns into the stable. Punk as the anti-establishment sort of guy is the guy to take them down. He goes over the likes of Jericho & HHH clean (yes Hunter, you're going to lose a match clean with my booking you egotistical ****) and becomes a super-face. During his next reign he changes the championship look, goes back to Mr Attitude & keeps rebelling against authority.