I think the first step would be to create a stand-alone build file which will produce a WAR. Do this before attempting to import the project into InteliJ.
I would use Maven. Creating a maven POM file to create a WAR is almost trivial and you can easily override the the default locations for your src, conf, and web content to match you existing src directory. Then test the build by deploying your newly Maven created WAR to Tomcat. I wouldn't think this first task would take more than a half day (at most a full day).
IntelliJ has a built in utility to import Maven projects. Then you should be off and running....
Regardless of the IDE you finally settle on, your project will be much better off in the long run for the Maven migration.
You initial Maven POM file will look something like this...
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>com.yourcompany.yourapp</groupId>
<artifactId>yourapp</artifactId>
<packaging>war</packaging>
<version>1.0-SNAPSHOT</version>
<name>Your project name here</name>
<url>http://maven.apache.org</url>
<dependencies>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>3.8.1</version>
<scope>test</scope>
</dependency>
<dependency>
*** other dependencies here ***
</dependency>
</dependencies>
<build>
<sourceDirectory>src</sourceDirectory>
<resources>
<resource>
<directory>conf</directory>
<includes>
<include>**/*.xml</include>
</includes>
</resource>
</resources>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<version>2.0</version>
<configuration>
<webResources>
<resource>
<!-- this is relative to the pom.xml directory -->
<directory>WebContent</directory>
</resource>
</webResources>
</configuration>
</plugin>
</plugins>
</build>
</project>
*** This is an example POM only... It's just meant to get you started and may not work "as is".