Hi Roelof,
HTTP request timeout you could set by using a HttpMethod instance and invoking HttpClientSupport.applyHttpSettings() on this instance and Settings instance that's modified to suit your timeout. HTTP connect timeout cannot be specified currently. We might add it in future versions.
WSS signature/encryption/username can be manipulated by manipulating WSS configuration via DefaultWssContainer instance returned by WsdlProject.getWssContainer() method.
Input parameters can be set for REST requests using setPropertyValue() method. If you want to set values inside a SOAP request, you need to modify XML document using lower-level methods.
I hope this helps.
Cheers!
/Nenad Nikolic a.k.a. Shonzilla