by definition a kilt is a specifically designed skirt worn by men, so in the most technical sense, it is a skirt.

as for the questions:

Do you think it is important to draw a line between Kilts and Skirts?
Yes. Skirts are worn by women and those who care to wear women's clothing. a Kilt is a male garment.

Do you think people will percive you as a Transvestite if your in an Unbifurcated garment?
only by the most conservative of folks, and even then I doubt it

Do you find you keep having to tell people your not in womens clothes?
No.

Is it seen as taboo to wear Unbifurcated clothing in public?
I wouldn't say it is taboo. It more unexpected than anything else. Most people who talk to me about the kilt offer either compliments, questions about most thinks kilted/scottich, or both!

basically wear the kilt with your head up. Realize that while it is simply a piece of EXTREMELY comfortable clothing on one hand, on the other it can be viewed as a visible demonstration of your individuality and willingness to be yourself regardless of social interpretation of your clothing choices.

above all else, wear the kilt because you want to, and enjoy it!