She feels that she is not happy in her marriage

Praise be to Allah.

Firstly: 

It is clear from your question that the psychological effects of your former life are still dominating the way you think and act. You mention something about the emotional scars that you suffered for many years, and it is as if you were waiting for your husband to compensate you for all the pain of the past. When you did not find that with him, you felt frustrated and that exacerbated your sense of not being cared for or loved, and this is the main cause of the problem. 

One would expect that in the past you would have learned the most important lesson of life, which is that one should not rely on people in order to attain inner happiness, and one should build social relationships on a foundation of values and morals, not on the basis of emotions and feelings of lack and need. For example, if you make friends with a woman, you should make friends with her and be kind to her because Allah, may He be glorified and exalted, loves those who are kind and because sincerity is one of the good values by means of which a person is raised in status before Allah, and not because you need that woman or because you expect her to show you a great deal of love, or because she shows you love and kindness in return. This is not the basis on which the Muslim should interact with people; rather he should interact with them on the basis that Allah, may He be glorified and exalted, loves him to live and mix with them on that basis, and not to expect mercy, love and care from anyone except Allah, may He be glorified and exalted. 

We understand that it is something very natural for a person to expect love and kindness from others, especially those to whom he has himself shown love and kindness. But this expectation should be built on a basis of strength and confidence, not weakness and lack of confidence, in the sense that one always expects the course of compassion between people to falter and for the exchange of sincere emotions with the closest of people to fail, so that he will make himself get used to the values of kindness and sacrifice, and he should deal with them on the basis of kindness for the sake of Allah and to remember that He is always watching him in his dealings with people, as Allah described the kindness of His slaves in the verse in which He says (interpretation of the meaning):

[Saying], "We feed you only for the countenance of Allah . We wish not from you reward or gratitude.

Indeed, We fear from our Lord a Day austere and distressful." (al-Insan 76:9-10) 

Secondly: 

With regard to what you mention of your husband’s falling short in regularly offering the prayers on time, this is his sin and not yours; it is his disobedience and not yours. We affirm this to you because we got the impression from your question that you feel as if Allah, may He be glorified and exalted, will call you to account for his shortcomings. But that is not correct at all. All you have to do is offer advice with kind words, at the right time. Then if he improves, praise be to Allah. Otherwise, we do not advise you to cut off ties with him because of a sin or shortcoming. The way people are and the way life is nowadays requires us to think more realistically and to constantly look for the best, then the next best, and to choose the most appropriate, then the next most appropriate of what life offers us (in other words, we should be willing to compromise sometimes). 

You should understand that the weakness of communication between you and the long intervals between meeting are the main cause for what you are feeling, especially since this separation occurred very early on, after only three months of marriage. Such a separation usually leads to a cooling off in the relationship and a decrease in attraction between you, as well as misunderstandings, negative thinking and a lot of insinuating whispers, let alone the physical changes that occur at the beginning of marriage. All of that helps to increase the feelings of distress and grief that you describe in your question. 

The remedy to that begins with appreciation of the blessings that Allah, may He be glorified and exalted, has bestowed upon you, starting with marriage, and realising that marriage inevitably involves some problems, and that perfect happiness can only come in the Hereafter. Rather in this world we should look for relative happiness within the framework of striving to please Allah, may He be glorified and exalted, and within the framework of family and social relationships, focusing on what we love to do and what we think is beneficial for ourselves, our communities and our ummah. 

This requires you to begin a new communication with your husband, forgetting about the past and putting up with any annoyance or trouble that you may go through because of him. You should try to take the initiative in being kind and gentle, overlooking mistakes and forgiving him. Try to work with him to find a solution to the problem of being far apart, because lengthy separation is definitely a cause for all of the psychological problems that may arise between spouses. You have no choice but to look for a solution to this problem, either by him coming back to stay with you in the country where you got married, or by you moving to join him. You should both look together to see what is easier for him and for you, and what is most appropriate for both parties, then do that. The more you show initiative and express a desire for connection and kindness, and keenness to be with your husband and to join him, the easier you will find it, and the more effective you will be in mending the relationship between you both, and helping your husband to get rid of his ill-feelings and encouraging him to start over with you. And who knows? Perhaps Allah will cause something to happen, and perhaps He will reconcile you with your husband in the best way; perhaps Allah will guide him thereby and make him more religiously-committed and a better person. So try hard and do not spare any effort to achieve that. 

At the same time, you should train yourself to be patient and exercise patience, and you should fill your time with beneficial deeds, of which there are so many, and develop yourself and your skills, which we all need to do – especially if you are in a country where there are a lot of opportunities for learning, training and acquiring new skills, or getting involved in voluntary charitable activities, in gatherings of righteous women and Islamic centres that are run by trustworthy people. 

So do not fall short in filling every moment with something good, and after that, if Allah wills, you will find a good outcome and a positive impact on all your social relationships, and on your relationship with your husband which you should take care of and overcome all the unjustifiable negative thinking that you mentioned in your question. 

We ask Allah to guide us and you, and to suffice us all and protect us from all ills. 

And Allah knows best.