Good that you are starting your prep so early.
1. It will definitely be good if you can get some research experience related to your research interest (or to those of the profs in the schools that you are keen in). Nevertheless, any research experience is better than none.
2. 3 years undergrad program shouldn't be an issue in most schools - furthermore, you graduated with honors. But check with them directly. I also graduated from a 3-year program and have no master. I contacted the schools and all gave me the ok to apply. Of course, I would be less competitive than other applicants who have master degrees.
Generally, based on your profile, you are definitely competitive for most schools. It is important that you do well for your GMAT to maintain your competitiveness.
For schools selection, I suggest you look at those that have faculty doing research in your interest. You can use the USNews or BizWeek B-School ranking as a starting point - but be aware that these are rankings based on MBA and not PhD programs.