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Do you want to create a custom firmware or install one? If create, google pwnagetool or snowbreeze + 4.0.1 firmware for instructions. If you want to install one, not possible on a 3GS with new bootrom.
 
I want to create and install one as I do not wish to use JailBreakMe.com. I have my shsh files saved for 4.0.1 if that makes any difference?
 
I want to create and install one as I do not wish to use JailBreakMe.com. I have my shsh files saved for 4.0.1 if that makes any difference?

That's a negative on installing a custom firmware with a new bootrom. And, why don't you want to use jailbreakme.com? It's an untethered JB.
 
You can remove Cydia. Don't see why anyone would want to. Why not just hide it if it bothers you that much?
 
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