Boxer's difficulties results from not being able to understand how his loyalty can be manipulated by Napoleon. The idea of Boxer pledging full loyalty and commitment to the life and politics of Manor Farm as well as not seeing how this can be twisted by those in the position of power creates difficulties. I think that Boxer is extremely loyal and believes in the authenticity of "Comrade Napoleon." Yet, without a sense of skepticism about government and those who rule, Boxer is used in a cruel way. Working more and more with greater difficulty as his health begins to fade, Boxer is "sent away" and becomes another statistic in the machine of government. The difficulty here is seen in loyalty and the lack of power that it contains. This is to say that when one is zealously loyal, there is little in way of being able to "pull back the curtain" and question authority structures. I think that this is where Boxer is and represents the difficulties he faces.
Boxer is probably the hardest working animal on Animal Farm, and perhaps also the most loyal to the "leadership" and "vision" of what the farm could become. His "I will work harder" mantra shows that he is willing to put forth the effort in order to benefit the farm as a whole, which could symbolize the ideal worker under a communist regime. "Napoleon is always right", his other quip, shows his blind obedience to authority, which is another admirable trait according to those who abuse power.
As far as adjusting to the "new lifestyle", I suppose this might depend on to which section of the novel you are referring. As the novel progresses, the other animals seem to spend less and less time working for the "common good", so Boxer is forced to take on added responsibility and burden, despite his declining health; after a while, his health fails him and he's sent away.
Throughout the story he is too uneducated to understand what is going on around him, so he believes that just working hard and doing what he's told will be a benefit to all. This, unfortunately, ultimately leads to his demise.