Lab404, I dont think all the questions are answered.
1) In your post you said "so far it has been a bit confusing; with different rules based on a foreigner's religion," To what are you referring? What info have you gotten out there that your religion has anything to do with anything? Unless.....if she is muslim and you are not, then there is the issue of your conversion before marriage---is this the case here? What race and religion is she? The marriage methods wont be the same for each.
2) As Roti says, you can apply for a visa to stay (LTSVP) but on the first go, if I recall its not a multi-entry pass so you have to stay here its term. What the government does not want is a wedding, followed by the groom leaving. If you do that, you will forfeit the LTSVP and have to start all over. Further, and this is a separate issue, under the LTSVP your wife is your sponsor and as such, she has to provide the qualifying income in the application process, not you. Is she working, with provable income?
3) The confusing part (for you) is the LTSVP vs. 90-day tourist visas. If and when you get the LTSVP, there are no more 90-day visas because its been replaced by the LTSVP. Also, also....if I recall, when you apply for the LTSVP, you cant leave even though its not yet been approved. Immigration will grant you (at cost) extensions to your current tourist visa until the application is approved. This means that, for example, if the paperwork, her income, etc., are not in order, causing delays, they will continue to extend. If you didnt figure on that and need to go out, the application will die. So, youd want to do this when you have nothing but free time in front of you and no need to leave at all.
4) I have to reiterate that last point. Try to see it from the governments perspective. For giving a marriage and a method of staying, they rightfully expect the foreigner to be in love and want to make a life here. If you marry and go, then from their perspective why did they give those things? So, this gives you two choices, although there may be others. You can please the government and come, marry and stay. Great! If not, then on the second go of the LTSVP (this will be longer than the first term of six months) which is now multi-entry, take your wife and go. There are at least two kinds of foreigners, those that want to stay in Malaysia, and those never intended to live here but want the marriage and future with the person and in those cases they marry and shift somewhere else. The problem with visas, especially like the LTSVP, is that one becomes a prisoner to them, its this cloud always hanging overhead. Its a two-edged sword and can be a hateful thing.
5) Another point about the LTSVP. Remember, she is the sponsor, its her application, income, paperwork. You are out of it except that you are doing all the work in the background. When you get to Immigration, she is the one doing the talking and submitting papers. She will qualify for the initial 6-month pass, AND the subsequent passes, too. This means she has to keep up her income and qualifications to be a sponsor, all of the time of the pass--potentially forever. The government steps you up gradually--six months, then two years, then five years--during which they look at your situation and confirm in their own minds you have a real and true relationship and marriage. Frankly, I dont know why they care SO much, its not like USA where the spouse has the potential to grab welfare payments and other benefits. In Malaysia, you get exactly nothing except the pass. Its ironic, or something, that they want the benefit of passes and relationships to flow to the malaysian and the country, but you the foreigner are not part of the qualifying process. So, if a filthy rich foreigner wants to marry a dirt poor Malaysian, I cant see a way how that could be done. Yes, ironic or what?