First of all i would check out if the developper of that JAR has provided the source to the classes. This reduces the possibility of JAD not beeing able to fully decompile all the class information.
However once you have all the .java files (including your changed or added class) you can let eclipse build the jar file as follows:
1.) Compile the .java files (Project -> clean..)
2.) File -> Export -> Java -> Jar file (click next)
3.) Select anything that belongs to the jar, input a name and click finish (Note the checkbox that says to export generated class files and resources).
Regarding Ant/ Maven and stuff: Those are just tools that help you. The same result you can archive by opening a console and use javac.exe to compile you can use ant or maven to compile your classes. Its just a matter of configuration.
I recomend you skip Ant right here and directly do the Maven in 5 Minutes tutorial :)