It's possible that the frame is bent if you rode it without either of the forward engine mounting bolts, but not guaranteed.
The simple answer, if you have no tools, is to take the bike to a qualified shop and ask them to fix it. I'm confident that most people could manage this if they had access to the proper tools and a place they can get away with working on the bike for an hour or two, but I've lived in an apartment before, and I can imagine what that's like. Anyway, here's what the shop you take the bike to will do:
0. Put the bike on a rear stand, or support it via the swingarm with jackstands.
1. Remove the lower fairings.
2. Support the engine from underneath with a floor jack. A scissor jack from almost any car will work, if you just can't get your hands on a floor jack. Be sure to put a block of wood on top of the jack so it doesn't damage the oil pan.
3. loosen the nuts on the ends of the rear engine mount bolts, but do not remove them completely.
4. Turn the heads of the rear engine mount bolts just a little - maybe ten degrees. This will loosen the engine mounts, allowing the engine to be loose within the frame.
5. Raise the jack under engine a little, install the forward engine mount bolts, and torque to spec.
6. Turn the rear engine mount bolts back until they're tight, tighten their nuts, and remove the jack under the engine.
7. Take the bike down off the rear stand and test ride.
If the frame is bent, no amount of raising the engine with the jack (step 5) will be enough to align the forward bolt holes. If that's case, consult a dealer or competent mechanic. The frames on these bikes are aluminum, and once they're bent, there's no truly safe way to bend it back into the proper shape.
Edit: The process I described assumes that your 2013 is similar to my 2005. Your mounts may be a little different from mine, and thus may not be exactly as I've described here. That said, the process is likely to be more or less the same.