If I am willing to repeat major courses, that I passed with a D grade, will they look bad on my transcript while applying for graduate school? I am a student majoring in civil engineering and I am in my  3rd year.I had a harsh beginning: I took 2 intensive courses during my first year of college after a gap semester. I didn’t perform well during my first and second year of college. I have repeated one failed major course( got a D- the second time)  and one physics course passed with a D( I got a C the next time). I have withdrawn from a surveying class during summer and retook it the next year. Recently, during the last semester of my second year I decided to work hard in order to raise my GPA and I achieved a score of 84.64 on my semester average. 
However, I am regretting and overthinking what happened during the first 2 years so much that I think that the only solution to relieve myself of the pain of thinking and blaming would be to repeat the courses that I passed with a D( 5 courses: one of them is a social elective, one an environmental chemistry core course but important for my graduate field of interest, and the three others are major courses: geology, mechanics of material and mechanics of fluid).
Which is better, to move on or to repeat these courses? Or to audit them? ( I am asking in term of graduate admissions).
My GPA is 2.92 over 4 which means 77/100. 
In my university, 80 is 3.2 over 4.
I don’t follow the lettering system
Yes, they will look bad unless the university replaces the old grade with the new one as some do. And if you continue to get poor grades in important courses it will look worse. But there are a number of other factors that people might consider, provided you can get them to look at an application. 

First, starting out on the wrong foot isn't uncommon. Nor is it a sure indicator of future failure. But, you need to turn it around. 

Next, people evaluating your record are more likely to put emphasis on what you've done recently than on what you did earlier. So, re-taking the courses, not for the grades but for the knowledge can help. And not having the knowledge will be a sure block to your future. Audits are less valuable, of course, as there is no record of your performance. 

Those evaluating applications for further study or for a job are looking for indicators of success. If you can show that, then you have a chance. A record of doing better recently will help, but it will also be important to have letters of recommendation from people who can honestly say that the past is past and you have a high likelihood of success in the graduate program and beyond. 

On the other hand, you will be faced with stiff competition from people who haven't had a once-deficient background. It is easier for evaluators to pick people who have always seemed to be a success than someone who has struggled. The decision has less risk when you choose an all "top marks" student. But, people know, also, that such "top" students don't always succeed and some people with special motivation will, especially if they have learned to overcome a weak background. 

So, the bottom line is that it isn't impossible, but it will be hard. If you can turn it around and convince your current professors that you truly have put yourself on a better path, then you have a chance. 

I'd also suggest that you don't "make excuses" for the past, but face it honestly. But get on the path to success and convince others that you have.