Hi Kamran,
I haven't had a ton of experience with bacterial conjugation, but the question you raise is an interesting ones.
First, a few potential roadblocks that I spot. It seems to me that you are mostly focusing on gastrointestinal conjugation (several groups of bacteria will never conjugate with gut flora), and as mentioned above, in such cases where strains like O157:H7 are present, antibiotics to clear out the virulent bacteria are generally preferred even though they are still toxic to the normal flora. O157:H7, along with a few other strains, is particularly nasty because it produces Shigella-like toxins that selectively target the larger ribosomal subunit of our eukaryotic cells (interestingly enough, this is the reverse of several of our antibiotics--many antibiotics work by blocking the prokaryotic 30S ribosomal subunit, preventing the bacteria from producing proteins and ultimately leading to cell death; imaging the 30S subunit was actually just recently awarded a Nobel prize).
It further seems that your project would be limited even in the types of gastrointestinal bacteria it deals with. Certain bacteria like cholera actually produce toxins that trigger the body to wash out the normal flora, and in such a case, antibiotics would definitely produce more good than harm.
Nevertheless, this actually makes it easier for you to do a project at school since it seems like the simplest bacteria to work with would be E. coli. This article posted above (
http://www.ncbi.nlm.nih.gov/pmc/article ... 1-0636.pdf) seems promising in blocking conjugation--be careful though, this seems to mostly be dealing with the donor bacteria, not the recipients that you want to target, but is still a start in terms of understanding the genes involved in conjugation.
Another route to blocking conjugation may be to get the bacteria to produce and secrete an enzyme that catalyzes the F factor (I'm not sure this is known, I'm looking into it, but imaginably such an enzyme exists).
Also, another thought off of the top of my head is the maping of E. coli genome. I know that to do so, they used bacteria that were especially selected for high frequency conjugation to initiate conguation, and they then interrupted it via a blender or some kind of force. Obviously that would not be a valid strategy inside of the gut, but looking into the specific mechanism of interruption (eg force, disruption of certain enzymes) may provide some clues as to more ways to interrupt conjugation.
Hope this helps,
Aaron Lin
that I can't stop 
How can I find a university professor to ask my question from him? and how should I start being in contact with them?