Can I still be a Catholic if I don’t believe everything in line with the church?

I think it's like asking if you can still be a STAR WARS fan if you don't think Ewan MacGregor was the best choice to play Obi-Wan.

The Church is like a book-club (they were actually CALLED "people of The Book" when it started). Priests are 'experts' in the book, but they are not 'the authors.'

Whatever is held by the Catholic Church to be dogma, must be accepted to be a Catholic. This includes many aspects the nature of God, the Incarnation, the sacraments, and salvation.

Neither "sola scriptura" nor "sola fide" as understood by Protestants can be held by Catholics. However, in the case of "saved by faith not works" most do not understand really what the Catholic Church teaches on that point (i.e. the Catholic Church doesn't teach that we can merit salvation by our acts and does teach that Salvation is a gift through Grace).

Before you contemplate any serious changes, ensure you have a good grasp of what the Church teaches on the topics you appear to disagree with and furthermore why the Church teaches what she does. There are loads of books and podcasts that can explain these doctrines.

I think the answers provided are valid, interesting, and helpful. So I will try not to double those, only add some details:

First, Lumen Gentium, the dogmatic constitution on the Church, explains that the Catholic Church is necessary for salvation (14). Then it goes into great detail on the matter of who exactly is, to what extent, a member of the Church. Those who are Christians but not in full communion with the Catholic Church, are seen with great respect. That doesn’t mean the Church any longer teaches that however close one is to being Catholic, one must, or maybe better should, join the Catholic Church.

However, Lumen Gentium is rather harsh about those who are Catholic, in the words of the council:

All the Church's children should remember that their exalted status is to be attributed not to their own merits but to the special grace of Christ. If they fail moreover to respond to that grace in thought, word and deed, not only shall they not be saved but they will be the more severely judged

So, one may come to the conclusion that on the one hand, the Church is rather open-minded about Her connection with and respect for all people of goodwill, especially those Christians who are not Catholics. On the other hand, She is not as open-minded to Catholics who do not truly “belong”.

Second, even though it has been said in other answers, I still would like to stress that you may need some study on the subjects you believe to be “not Catholic”.

Sola gratia may be less far off the Catholic teachings on grace, and the duty of the believer to respond to that grace.

Sola scriptura most definitely is not Catholic, but in your words, I read respect for scholars. That may be a good starting point to research your exact beliefs and the exact teachings of the Church. The Catholic faith is not what we call “cadaver discipline”, I don’t know the English wording for it, but it is something like believing without using your own brain.

All sources can be found on the website of the Vatican. Documents of the Second Vatican Council

I think the extremely terse, unhelpful answer to "...can I still be Catholic" is "no". (See also eques' answer.) The slightly longer answer is "if you don't agree with their teachings, do you really want to be Catholic?".

However, while that's a technically correct answer, it isn't really helpful.

Biblasia noted in a comment:

Martin Luther was one of the first Catholics to hold some of the views you expressed, such as righteousness by faith, not works.

Luther and others eventually started what is now known as the Protestant Movement. Based on some of the comments in your question, I would encourage you to learn about Protestantism, the reformers and the reformation, and the beliefs of various Protestant groups. Note that some of these groups are quite divergent from Catholicism, perhaps even differing to a degree which you might find uncomfortable. Lutherans and Anglicans are going to be the most similar, as their beliefs and practices are less divergent.

As far as baptism... you may or may not be aware there are two separate rites; baptism and confirmation. Most Christians believe baptism is necessary or at least extremely important, while confirmation may be less emphasized or even (in more liberal sects) ignored entirely. The reason this matters is that Catholics (and most other Trinitarians, AFAIK) regard any Trinitarian baptism as valid, and also because baptisms (at least in my experience) typically only require you to confess either the Apostles' or Nicene Creed, which are similarly upheld by the majority of Trinitarians. By contrast, confirmation is a confessional acceptance of the teachings of a specific sect (e.g. Roman Catholic).

Now... you should absolutely talk to a priest/pastor. If you can, I would encourage you to share your concerns with both the priest at the Catholic church you're already associating with, as well as one or more Protestant pastors. You should ask them if it's okay to get baptized (not confirmed) if you have doubts about Catholicism. I would specifically ask the Catholic priest if it would be okay to deliberately go to a Protestant church to be baptized due to your doubts, and similarly I would ask the Protestant pastor(s) if it would be okay to be baptized Catholic.

The best thing, obviously, is going to be to find a church whose beliefs you feel are Scripturally sound and to be baptized (and married) there. However, I think it's more important to be baptized at all than to agree 100% with the church where you are baptized. Don't get too hung up on perfection; you aren't going to do everything right, which is why Christ died for you! What's important is that you are continually seeking God and that you accept His free gift of forgiveness. As long as you've been forthright about your concerns beforehand, if a) the person baptizing you isn't worried about your baptism, and b) you agree with whatever you confess upon being baptized (i.e. probably one or both of the main creeds and perhaps some other, relatively superficial stuff that nearly all Trinitarian Christians agree with), it's probably not beneficial to worry unduly.

When it comes to confirmation and communion (Eucharist), however, there you might want to hold off until you have a better understanding whether or not you agree with the church in which you'd be participating. Not all sects make a big deal out of such things, but others take confirmation and communion very seriously as declarations of a Christian's agreement with a specific theology.

So, to summarize and circle back to the question that really matters:

Does it matter what type of Christian church I'm baptized through if at the end of the day what I'm being baptized [into] is Christian?

I hesitate to say it doesn't matter at all... but I believe many Christians, and Catholics in particular, would agree it's far more important to be baptized than to be baptized in the 'right' church.

Okay, a disclaimer and a bit of an aside. I said "many Christians" above, because some sects (ahem: Baptists / Pentacostals are probably the best known in this respect) have somewhat divergent views on the significance of baptism and its correlation with "making a decision for Christ". These sects might not accept a Catholic baptism and might insist on someone 'transferring' into their church being re-baptized according to their particular formula.

The Roman Catholic church specifically considers any baptism valid so long as it uses water and the Trinitarian formula (details and a list of sects recognized by the RCC as performing licit baptisms). I would expect many (though likely not all) sects to use similar standards, i.e. a fair subset of Christian sects would mutually respect each others' baptisms.

Another point to keep in mind, although not relevant in your case, is that many Christians practice baptism of infants, while others consider this practice invalid.