I did it myself in NJ last year and the hardest part was the initial paperwork, but it really wasn't that bad at all. The CIS form is the hardest to figure out since there is <name> vs <name>. (You use INRE: <your old name>) in that field. The judges secretary called me up and helped me through it all, but I had everything in order anyway. (Other people I know that went through the process didn't get as much personal contact with the court, but I did put being transgender transitioning from Male to Female as the reason for my name change.)
You will have to disclose any pending charges even though they are in a different state, but as long as your honest about everything you shouldn't have an issue. If something changes on those pending charged from the time to file till your court date (typically 4-6 weeks) you can address them on your court date. The court will simply require you to notify the other jurisdiction of the pending case of your name change. However you may need proof of that. On the form there is a part for NJ pending courts cases or probation (if that applies), and that could be used to notify the other jurisdiction even though they are out of state.