Much of his fight has centered on the idea of placing teams in divisions where they compete against programs of equal male enrollment, of equal squad size and of equal ability.
Mathematically speaking, the Colonials have been at a slight disadvantage in the 16 years they have been in YAIAA Division I.
"This is my sixth year as head coach, and I've always said our enrollment has paralleled that of a West York, a Kennard-Dale and a Susquehannock," Muller, the president of the YAIAA Football Coaches Association, said of those Division II teams.
New Oxford's boys' enrollment usually hovers around the 450-470 range, typically placing it in Class AAA. Similarly, five of the six Division II teams in 2009 were in Class AAA while six of the eight Division I teams were in Class AAAA.
So, on paper, New Oxford has always been among the low men on the totem pole in the YAIAA's biggest division.
After a number of realignment proposals were looked at in the winter, the latest was approved this season. And the Colonials will benefit, shifting to more equal footing in YAIAA Division II.
Five YAIAA teams were realigned into different divisions in 2010.
Dover will join New Oxford in Division II from Division I. And Eastern York, Littlestown and York Suburban will bolster Division III from Division II, creating the league's biggest
As for the Gettysburg Warrior football team, it was realigned into the Mid-Penn Colonial after spending the last decade-plus in the Mid-Penn Keystone. It entered the Mid-Penn in 1993 after the Blue Mountain League broke up.
And for the factors that contributed to the switch, enrollment wasn't a big issue.
Gettysburg annually faced the likes of Hershey, Lower Dauphin, Susquehanna Township, Mechanicsburg and Palmyra. All five of those opponents were Class AAA schools, just like Gettysburg.
Instead, more important was location. Mid-Penn Executive Director Fred Isopi said in February he tried to accommodate Gettysburg and other schools by putting them closer together "geography-wise."
Even better, not only will the switch save travel time and cut fatigue, but it will also save Gettysburg close to $12,000 in transportation costs, Gettysburg athletic director Carlos Wampler said in February.
"A lot of people around the community are sort of excited," Wampler said. "It reminds them of the old Blue Mountain League. I think one of the attractions, when I presented this to all the coaches, was that in the high profile sports we'll play those same schools."
Gettysburg's southern roots linked them up in the Mid-Penn Colonial with western neighbors in Franklin County. Three among them, James Buchanan, Waynesboro and Greencastle-Antrim, could become their biggest rivals in the future.
"I think we'll still attract a crowd," Wampler said of the switch, which could be viewed as a demotion to some. "I don't think we lose any luster (from switching conferences)."
So much for being the underdog: In New Oxford's case, an ironic twist occurred when the PIAA came together to discuss school classifications for its new two-year cycle in 2010-11.
It deals with the very concept Muller strived so hard to accomplish.
After the PIAA met, a decision was made to bump New Oxford up to Class AAAA in 2010. So ironically, New Oxford will become the enrollment bully in Division II, while the others will be fighting to keep up.
Muller says the reason for the bump is the school's freshman class, which he says is the biggest in school history. However, class sizes are static from year to year, he says, so he believes the Colonials are in the position to go back down to Class AAA when the PIAA meets again.
"I look foolish now because I fought forever to get down (to Division II) and now they re-did the numbers and we're quad-A," Muller said. "Figure that. But I still think (Class AAA is) where we're going to be. I think that's where we need to be."
How about the results?: While much will be made about the change, Muller and Gettysburg High first-year head coach Ray Gouker don't believe their opponents will be all that different.
Muller expressed the same concerns about the quality of West York, Kennard-Dale and Susquehannock that he would have if he were playing William Penn, Dallastown and South Western.
In fact, New Oxford's 2010 schedule could perhaps be its toughest in years. The Colonials still have dates with Division I incumbents Central York and Red Lion, plus non-conference games against Division III Delone Catholic along with Greencastle-Antrim and Waynesboro.
"Just because we're not playing those quality teams doesn't mean teams on our schedule aren't quality," New Oxford's offensive coordinator, Joel Brosius, said. "We still have Central York. We still have Red Lion. Those are two teams we've played forever. I'd be hard-pressed to think anyone thinks West York would be an easy game. So there's just as many tough teams for us."
Then again, New Oxford's small nine-game sample with Division II teams over the last six years has been promising. The Colonials were 6-3 against the competition, including a split with West York.
As far as Gettysburg is concerned, Northern, Waynesboro and Shippensburg aren't pushovers either. The switch in leagues could begin to shape the team's new identity without former head coach Sam Leedy, who retired last season after leading the team for 20-plus years.
"The people that we are going to be playing are going to put 11 exceptional individuals out on the field," Gouker said. "We're going to have to be at our optimum to beat them. So we'll have to be sound and know our scheme. Our kids will have to know their assignments."
Both New Oxford and Gettysburg will find themselves on new ground in 2010, facing different opponents on different fields.
The surroundings may feel foreign, but the game's intensity will remain.
"I don't think it'll be any easier," Muller said. "I just think it'll be a new challenge for our kids."