I figured it out and will be writing a full tutorial with images in the near future to explain this insane re- scale technique but for now here is a rough explanation of the technique. I think this could be turned into a Zscript that could automatically preform what can be a very time consuming process.
Problem- You have multiple Ztools with appended subtools that are at vastly different scales from one and another when appended together as subtools or brought together in an outside program (IE maya, Xsi,) Logic would dictate that could use Subtool master to change the scale using the scale defromation in Zbrush, but if the scale change is too large (over 100 percent) you will get very crappy results (See below image) once Tpose>subtools is applied.
http://forums.cgsociety.org/attachment.php?attachmentid=167766&stc=1
Solution>
Setup - Export your ZTOOL at a low SUBD level as an OBJ ( making sure tool>export settings are set to 100 for scale and 0 for offset) to your 3D app of choice and using a keyframe locator or group, keyed at a scale value of 1 and an XYZ of 0 on frame 1, parent your object under the group and on frame 2 scale the group to the correct object size, adding a keyframe on Position and Scale once you arrived at your properly corrected scale. Now your ready to correct the size of your high rez Ztools
1 - Export each your subtool at the highest SUBD level as an OBJ, making sure tool>export settings are set to 100 for scale and 0 for offset. Your object will need good UVs in order to transfer your polypainting latter. You will lose any HD geometruy sculpting with this scaling method.
2- Import the Highres OBJ into your 3D, parent the High rez geo to the animated scaling group on frame 1, play forward to frame 2 to scale the object
3- Unparent your Highres OBJ, freeze scaling and translation then using GOZ send the mesh back to Zbrush, this will take a couple of minute if the objects are in the 1-2 million polygon range. and up to 10 minutes if the getting close 10 -15 million mark .
4- Once back in Zbrush you will need to got to TOOL> Geometry > Reconstruct Subdiv and rebuild the subD levels of your now properly scale Subtools!
5- Then if your mesh had polypaint you will need to create a texture map of your polypaint on your original Mesh (I go with 8K so I dont loos detail) and clone texture and load it onto your resized geo and polypaint>polypaint from texture at your highest subD level.
And now repeat this process for every subtool and you will have a size corrected model.
Now as word of warning It took almost 8 hours to transfer a 20 plus subtool model in this way ( I will admit I forgot to UV a couple of pieces so that added a couple hours) as well this is a memory vampire and I had to restart my PC at least 5 times as Zbrush would run out of memory on exporting some of 10 to 15 million polygon meshes. Id love to see this made into batch process that I could run on a machine over night or on multiple machines in order to speed it up. But my best advice is to make sure your object are scale correctly at the beginning of the modeling process not the end. There are some weird scaling issues with the 4R3 and I find it best to use GOZ for final export back to your 3d package to maintain the correct scale, the reason I have you export your Highres messhes instead of GOZing them was that my Zbrush would crash when send over anything over 10 million polys using GOZ. But I found that the best way to maintain perfect scale on the way back was to GOZ the corrected scale highrez mesh back to Zbrush (which the software seemed to handle fairly well)
PS I just saw that there is a new version of Transpose master and I will test it to see it geometry destruction issue is still a problem and report back)