Or is Subdrag's incomplete? Yours seems to extract more out of it.
SubDrag's decompressor only extracts compressed files. It's automated though, so he can handle a lot more games than Midwaydec at this point. Midwaydec needs filelists for each game, but that also means it can extract absolutely everything inside one.
So...
Yeah, Midwaydec grabs everything you put a line in it for.
Tested, and it looks like it will just decompress a file up to a certain filesize and ignore any extra data falling after it. So, if it's shorter you don't need to do anything unless you want to.
If you do need to edit the table...
VPK files only fall in a certain part of the SSB ROM. That filetable is at 0x1AC870.
Entry format: 0xC each
0x0 4 offset to data from end of table [1B2C6C]; compressed if negative
0x4 2 -1 if not present
offset in words in decompressed file for filetable (*4 for actual)
0x6 2 compressed size in words (*4 for actual)
0x8 2 -1 if not present
offset in words in decompressed file for resource data (*4 for actual)
0xA 2 decompressed size in words (*4 for actual)
If you're moving entries around you only need to change the values at +0 and +6. Take the actual size of the compressed file and divide it by four for the value at +6. Setting the offset takes two steps. Subtract 0x1B2C6C from its position in the ROM for the base value. If it's VPK compressed set 0x80000000. If you look at the table it's probably obvious what they're doing though.
I've been bogged down by an unexpected project but I'll try to write a little file inserter for you when I get some time. It'll be in python, but, well, aegh...