Glad you figured it out, but just to help others that may be debating this.
1) What would be the best option to encode these extra inputs (keywiz/ipac/minipac/...)
Personal preference based on features desired.
2) The 360's use USB, the Spinner uses USB/PS2, the Trackball uses USB/PS2, and the extra encoder uses USB and/or PS2. If I use USB for everything am I going to run into problems.
You want to assign different UID's (can be done in software) to each U360. (or plug them into different USB ports (pairs of connections)). Also would apply if you had two of the same model and brand or trackball, two of the same model USB mouse hack, two same model GP-Wiz encoders (for the GP-Wiz, you need to specify this when you order them.)
3) Can I run all these USBs into a hub?
Yes, you might need a powerd hub depending on how many devices you are hooking up.
4) Would it be better to get an encoder that accepts the extra switches + the trackball + the spinner and have only the 360's and the encoder going to the computer.
From your response, I assume you are using a PS/2 trackball (with built-in interface of some kind). Otherwise, I think your question is whether you are better with the mini-pac or the I-PAC and an Opti-Pac/Opti-Wiz, etc. This is also somewhat personal preference. The mini-pac is a better value, but somewhat harder to wire up . . .
One thing to consider - The 360's can be used either as a gamepad or wired through the I-PAC. You might want to check that any emulators you plan to use can accept gamepad inputs (either directly or through RBjoy or Joytokey, etc.), and then decide how to wire them up. For MAME it won't matter. If you wire them through the I-PAC, you lose 8 inputs, unless the sticks where included in your 28 above.