My question really is would attending a presbyterian seminary like this cause trouble for me to find a church after graduation? Would even a reformed congregation of the SBC look at a MDIV taken at a Presbyterian seminary as less desirable then a Baptist seminary, would there be prejudice? Would it be better to try to find a Baptist Seminary?
That depends on how Reformed the Southern Baptist church is. There are a lot of men and churches within the SBC that are varying degrees of "Reformed."
Many of them simply use the term Reformed to describe someone who adheres to TULIP, and in some cases this would include those who are shaky on the "L." In my experience, most of them, particularly the younger men, are not dispensational in any sense. But many of them are also not covenantal, with something like New Covenant Theology being fairly common even if they don't identify with that label (think Carson, Schreiner, Piper, etc.) Sabbatarianism and any emphasis on the RPW seem to be pretty rare, even among those who are otherwise of a more covenantal bent. (Of course, taking exception to the confessional teaching on the Sabbath and having little appreciation for the RPW is not uncommon in the the PCA as well.)
If you are only going to be looking at those churches that would be strongly covenantal and more or less strictly subscribe to the 1689 you will be fine, although as I note above, I don't know how many such churches there really are in the SBC at this point beyond those that are dually affiliated with ARBCA. It seems that many in the SBC, even within Founders circles, are moving more in the "missional" direction (think Driscoll, Keller, Stetzer, etc.) and are not that focused on the confession.
On the other hand, if you want to leave your options open to be able to minister in a context in which a Southern Baptist church is becoming more Calvinistic or Reformed and is looking for a Reformed pastor to help move things further in that direction, you'd be better off attending one of the 6 SBC seminaries, with Southern being the #1 option and Southeastern probably being #2. The whole Reformed issue aside, I have known of SBC pastors who graduated from places like Dallas Theological Seminary having a harder time getting serious consideration compared to those who graduated from a SBC seminary because many SBC churches tend to look for a graduate of one of their seminaries. This can even be the case with some Calvinistic churches.
Generally speaking, I'd imagine that having a degree from a non-SBC school is probably going to be less of a problem the further you get from the South, where most Southern Baptist churches are. Ivan Schoen or some others in the SBC may be able to lend a more informed perspective to this question.
If you are leaning heavily toward ministering in a SBC context, I would also think that a SBC seminary would be preferred if you are interested in delving deeply into the particulars of SBC history and practice, much of which has a significant Calvinist influence, especially prior to about the 1920's. I'm not looking to denigrate WSCAL, but it would be more narrowly focused toward Reformed contexts. The Baptist emphasis (the IRBS site shows one Baptist History course) is likely going to focus heavily on English Particular Baptists, maybe hitting the high points of the American Baptists and perhaps the more recent Reformed Baptist movement. (I'd be happy to be corrected if I'm wrong here.)
Something else to consider is where you fit on the law/gospel issue. WSCAL has a particular emphasis on that issue that is not shared by all within the Reformed community. There have been some recent threads here regarding that. My guess is that their view is less popular among Reformed Baptists than it is among the Presbyterian/Reformed, and it is a subject of some debate in those circles as well.
Another Reformed Baptist seminary to consider is
Reformed Baptist Seminary in Greenville, SC.
It appears that you have some time to consider this, and it's good that you appear to be weighing your options carefully. It would be a good idea to contact those seminaries that you identify as possibilities and arrange visits to those you're most interested in over the next few years, if possible. This gives you a chance to sit in on some classes and meet professors and students.
