I've found a package that I want to use as a reference mesh for a new dress I've made. When I try to open the package in TSRW I get an error message that the "Index is outside the bounds of the array". If I play with the project settings the mesh will show up.and although all the sliders work, I can't select any of the other LOD's or export it -- that would be too easy! I'm trying to create a morph reference .wso from the package that TSRW doesn't like. FIrst, I exported my new LOD1 group_base wso as a .simgeom, renumbered it starting with 5000 and saved it. The LOD1_1 was treated the same way starting with the next vert ID in the sequence that showed in the ToolKit window and saved. That gave me LOD1 and LOD1_1 with good vert numbering. Those were converted to WSO's as separate files.
On to the simgeoms. LOD1 and LOD1_1 were exported from the original package with s3pe. Each LOD section was morphed using the bgeo. After each morph was done the 2 parts were imported into MilkShape, regrouped, renumbered starting with 5000, and saved as a wso. Rinse and repeat for each morph. The new ( what I thought was my reference mesh!) was then saved as a single wso. Before morphing I did examine both the new reference wso with ToolKit and as far as I can tell everything looks normal -- all morphs have the same face and poly counts, and the vertex data LOOKS fairly normal (no numbers with drastic changes from 1 sequential vert to the next).
Finally each new LOD segment is morphed with the reference wso I just built. When those newly morphed WSO's are loaded back into MS, they're completely exploded. My mesh is split into upper and lower halves at the waist but the morphed LODs both have legs on them. What am I doing wrong?

Yikes.

Looking at what you did - if you imported .simgeoms into Milkshape and exported them as .wso, the bones will probably not be right. There's some trick to doing this IMO but I don't remember it. A better method would be to:

1. Export the simgeoms from the package and create simgeom morph meshes from the BGEOs. (You've already done this)
2. Either import the geom meshes and morphs into Milkshape, regroup, renumber, and export; OR use the GEOM Frankenmesh function in Toolkit to combine the LOD1 and LOD1-1 with their morphs into one set of base & morphs, with renumbering.
3. Use the Toolkit / Conversion Tools / GEOM to TSRW to convert the base & morphs to a complete WSO.

Keep in mind that combining LOD1 and LOD1-1 will probably put you over the limit of 60 bones. Just the other day I was thinking I should add a tool to split meshes/morphs into parts when they have too many bones, since it looks pretty hard to do manually.