Well OK. I remember I had some trouble with it myself but it's been a while since I've done it so bear with me. I work with an uninterleaved ROM until I'm finished patching, then I convert it to Game Doctor format with the interleaving program provided in the patch kit.
First of all start with a good copy of the ROM. I started with an SMC version. Since you've been patching away on it run GoodSNES and make sure you have the golden version. It's easy to get it corrupted by some patch programs so double check it.
Make a copy of the golden version and work on the copy, always leave the original untouched in another directory.
Check the file size. You'll probably have to add an SMC header. The size with header is 6,291,968. Use SnesTool like it says in the readme to add the header if you need it.
Apply only one of the IPS patches to the ROM with SnesTool. I used TOP_DX2U.IPS. Now test the patched version. Yes -- test it. Load it up on an emulator an be sure it works OK. If it doesn't you messed up and you've got to start over.
Once you get the SMC patched version working use the TOPINT.EXE program to convert it to Game Doctor format then split it using insnest. Even though insnest has bugs it is generally the least bug free conversion and splitter that I've seen so use it.
Make sure you follow the GD ROM name conventions. My split ROM files are SF48077x.078. The first, SF48077A.078 is 1,049,088 bytes because it has a header, the rest are 1,048,576 bytes.
The GD header is 512 bytes. If you have trouble verify that the first part of the header looks like this when you're done:
47 41 4D 45 20 44 4F 43 54 4F 52 20 53 46 20 33
81 20 21 20 21 20 21 40 40 24 25 26 27 24 25 26
27 22 23 40 40 28 29 2A 2B 00 00 00 00 00 00 00
That should do it. Now that you know how, Fugazi, I appoint you the answerer of this question in the future.