JB via Spirit and now purchases won't transfer

This is a followup to a previous post in which I asked:

When I connect my iPhone 3GS to iTunes, iTunes asks me to upgrade to 4.01. But it recommends I transfer my purchases first. However, when I tell it to transfer my purchases, it syncs for like half a second then nothing happens. I know that my stuff did not transfer b/c when I try to upgrade it stil tells me that the same specific purchases have not been transferred. What's wrong and what can I do to make it work?

A helpful member responded:

"This is usually caused by a patch to the iPhone that allows hacked/cracked apps to install. If you have installed this package,uninstall it and reboot the phone, then attempt to transfer the purchases again."

So my follow up question is:

I previously jailbroke it when it was 3.1.3 using Spirit but I updated it to 4.0 and restored it. I did not jailbreak my phone again after I updated and restored. Did restoring it not delete all the hacked/cracked apps? If not, how do I uninstall the package?

Thanks!

Updating does not wipe the media partition. This means any apps, music etc are still on the iPhone.

Yes the jailbreak is removed. Traces remain.
Your only option is to find out which apps you have bought or updated directly on the iPhone. Repurchase these on your computer with iTunes (free to do this)

If you have bought music or video from iTunes on the iPhone - say goodbye to that. It can't be repurchased free. Maybe there is a way to fix that with an AFC2 client.

If you are lucky, iTunes might allow you to backup (not sync) your iPhone

Once you have backed up your files you need to restore (not update) to iOS 4.0.1 (unless you backed up a SHSH for an earlier iOS version). Then either restore from backup or setup iPhone as new (I recommend you setup iPhone as new)