if you have other system you can access the Websphere Application server(WAS) console using browser
there you have applications in that you can upload the war file
you probably might have to do changes in the code also.
because i have faced similar issue. some resources file like applicationresource.properties or some user defined xml files are not found by WAS.
you will have to modify application to read form a specific path.
Also please not that ibm uses ibm jvm to run it. you might be using sun jvm to compile war.
so please dont compile it in 1.6 and install it in ibm 1.5 jdk. use sun jdk 1.5 to compile.