In recent weeks this soft-spoken but resolute chairman has faced further criticism and venom as the club lurches into an early-season crisis. A vocal element want Johnston out. Marie Macklin, an energetic and opinionated Ayrshire business woman, has added her voice to the dissent. Bill Costley, a former club chairman, has embarrassed Johnston by claiming he once asked for £2.5m to sell his 87% stake: a claim Johnston vehemently denies. It is all becoming pretty hostile.
Meanwhile, one of the club's most popular managers in years, Kenny Shiels, is out of work, sacked by Johnston. His replacement, Allan Johnston, has yet to win in his opening seven games. Crowds are down, with some supporters saying they will not be back until Michael Johnston is gone.
Smiling warmly when we met yesterday, the chairman keenly reminded me of why he was at Kilmarnock in the first place. Jim Moffat, once a generous benefactor to the club, had handed his majority stake to his son, Jamie, who was not really interested in football, and who in turn handed the 87% stake - gratis - to Johnston. "That was in 2005, by which point, with the club's hotel built, there was a heavy debt at the company," explains Johnston. "Jamie was ready to put the club into administration but I said, 'hold on, I think I can take some measures to avert that.' The Moffats had left a legacy and put a lot of money into this club, and I wanted to protect that legacy, not to say the 200 club employees, so I happily stepped in.
"I don't have any personal wealth; I couldn't shovel money into Kilmarnock. But I knew I could protect the club, and what I had to do was embark on a series of cost-cutting measures. In 2005, the club was facing the stark reality of insolvency. No-one with any wealth was willing to save it. So I took the project on and began measures to save the company and establish a business plan with the bank. Here we are, eight years later, with the club still in debt, but down from £13m to £9m. We've made progress."
Not enough progress, though, to appease Johnston's many critics. Among them is John Gall, head of the company who make the Killie Pie, who stated witheringly this week: "Michael Johnston is single-handedly ruining Kilmarnock FC." It is the type of disparaging language Johnston has had to get used to.
People such as Gall, Macklin and Costley want Johnston to step down. But it is a complicated scenario, not least because he is not interested in relinquishing his shares. He remains a "one-man board", though he plans to change that soon. "It was always my plan to have a board of directors, if people were willing to come forward and invest meaningful amounts of money in the club," he says. "But such people have been sorely lacking up until now. Nobody in recent years has come forward and said, 'I want to give you so many thousands or millions to help.'
"People have spoken about 'taking over' the company, by acquiring my shares and becoming the principal shareholder. I have always said, 'look, fine, but why don't you invest in the company, so that we can work in partnership, and improve the club?' I can't do everything. But if people think they can do better, and attract more supporters or sponsors to Rugby Park, then I'm all for that.
"I have handed over some pretty confidential information about Kilmarnock FC, in terms of the state of the club and its debt, to one or two potential investors. And they ended up looking at it and saying to me, 'good luck, Michael, you carry on; we can't see our investment making much difference.' The problem is the size of the debt which, at £9m, is pretty large."
Johnston's detractors claim that, having acquired his shares as a gift in the first place, he should be willing, when the time comes, to hand over his stake in such a debt-laden club to someone else for free. It is a complicated argument which has caused him some grief, and one that he rejects. "I actually haven't had my shares valued," he says.
"But what I do know is that, in the past, some people in this present saga have either received money for shares, or asked for money for their shares, which valued them pretty substantially at a time when the balance sheet was very similar to the one we have now. Marie Macklin has put a price on her shareholding in the past which was in excess of £1 per share. Bill Costley, when he resigned as a director in 2002 - with a club balance sheet comparable to today - received a large proportion back of the money he had put in."
Costley, in particular, has been a thorn in Johnston's side, claiming the incumbent asked for £2.5m for his stake. The claim stems from an email exchange between the two, which Johnston says has been completely distorted. "I sometimes think I could spend all my time and energy suing people for misleading others," he says. "It is particularly disappointing when it is a previous chairman, who should know better and behave in a more dignified manner. Such statements are only designed to whip up resentment.
"Another falsehood Bill Costley perpetrated this summer was that I am taking £100,000 a year out of this company. It is just nonsense. For a long time I received nothing from this club. Latterly it has been something like £60,000. If you want to compare that to other football club executives, I think you'll find it compares pretty well."
And what of handing over shares, received freely, to someone else, freely? "It is a fallacy to simply say I got my shares for nothing," says Johnston. "I have now invested 10 years of my professional time in running Kilmarnock, for very little reward. In terms of fees or remuneration received, I often didn't charge the club anything for legal or secretarial services. But, ultimately, due to cuts to overheads, I have had to take on so many executive duties, and spend so much time on it, that I had to start charging the company some professional fees.
"If anyone says, 'Michael, you got your shares for nothing in 2005, why on earth would you get something for them now?' I would say, well, look at what I have done over these past 10 years, I think that has to be taken into account. The bottom line is, I don't want to sell my shares. I want people to come along and invest capital in the company, to come on board with ideas."
Johnston claims to have saved Kilmarnock around £50,000 in legal fees, about £300,000 a year in executive salaries (having cut those positions) and managed to reduce the debt from £13m to £9m. Under him, the Ayrshire club have paid more than £5m to the bank in debt-reduction, interest and charges. He inherited this financial mess and it only worsened through the banking crash and economic downturn.
Yet Johnston is a man battling to win the hearts and minds of the fans, not least in sacking Shiels, who brought silverware to the club. Also, crowds are waning alarmingly. "Removing Kenny Shiels was not a decision taken lightly," he explains. "Kenny was very popular with the fans, and he worked hard on that bond. But the results had become so poor we had to make that decision. We'd won one game at Rugby Park since February. We'd had our worst home record - a significant factor - in 30 years. I couldn't ignore it.
"The new manager has had a difficult start. He's trying to bed in a new team. And, in terms of the town, we are now in a very challenging environment. All the traditional industries have evaporated in Kilmarnock. We have lost our traditional support, most of whom worked in local factories like Johnnie Walker, Saxone, BMK, Glenfield and Kennedy, Massey Fergusson, Wilson Sporting Goods … the list goes on and on. Dozens of big businesses have pulled out of Kilmarnock, and every time one of them goes, we lose season-ticket holders and some corporate spend. So it is a very difficult market we are in."
What will make or break Johnston is a plan he currently has for fresh investment. Billy Bowie, an Ayrshire entrepreneur, is prepared to plough money in and join the board, and other figures are on the horizon. Something else is afoot in terms of a "solvency restructuring" which Johnston is keeping under wraps.
"I'm in discussion with a number of potentially interested parties who might be willing to come in as investors, as part of a restructuring of the club," he says. "It is problematic to talk about, because people I am talking to want to remain anonymous at this stage.
"I have only one ambition here: to improve the lot of Kilmarnock FC. That is why I am still here."