I need to know how, using windows scripting (preferably jscript) to
set environment variables such that the new values are immediately
available for new commands that are run.

I have a windows script (javascript) that sets environment variables
in the registry.  Here is a relevant bit:

var shell = WScript.CreateObject("wscript.shell");
// Set some string variables OMhome and append to the path
shell.RegWrite ("HKCU\\Environment\\TENA_OM_HOME",  OMhome, "REG_SZ"
);
shell.RegWrite ("HKCU\\Environment\\PATH",  path, "REG_SZ" );

Although this sets the values in the registry, the values are not
added to the environment until a reboot or until you view the current
environment using MyComputer/Properties/Advanced/Environment and click
OK.  This is verified by opening a CMD.EXE shell and typing set PATH.

Is there a scripting command to explicitly force Windows (Explorer?)
to reread a particular environment variable from the registry?

Set An Environment Variable Via WMI
From a Google post.

Note: this works great for modifying a variable for all Terminal
Server sessions as well.  The example below creates a variable named
%RouterStatus% with the value of UP in the SYSTEM  environment on a
server named Mort.  - AKA

SetWmiEnvVar "MORT", "<SYSTEM>", "RouterStatus", "UP"

Sub SetWmiEnvVar( Host, sContext, sVarName, sValue)
 ' Sets an environment variable on an arbitrary host via WMI
 ' NOTE: This will of course not affect currently running
 ' processes.
 ' For a systemwide value, use <SYSTEM> as context
 ' for default user, use <DEFAULT>
 ' otherwis,e use the specific user's name
 ' Get the class object itself
 Dim EnvClass, EnvVarInst
 Set EnvClass = GetObject("WinMgmts://" & Host _
  & "/root/cimv2:Win32_Environment")
 ' Make a new instance of that class
 Set EnvVarInst = EnvClass.SpawnInstance_
 ' File in the key props and props of interest on that instance
 EnvVarInst.UserName = sContext
 EnvVarInst.Name = sVarName
 EnvVarInst.VariableValue = sValue
 ' Write the new instance in to WMI
 EnvVarInst.Put_
End Sub