My New Harddisk had an unknown Windows Partition

The error message is clear enough to me, it has been posted 2000+ times here.

Boot Camp Assistant is complaining though that you have somehow gotten some files and the free space so it is not contiguous, is fragmented, and can't take the end of the drive partition to carve out a slice for a Windows partition.

It should have worked though. 98% of the time in the past, using SD to restore will result in a good setup.

Other potential issues I see:

Lion has additional hidden and user partitions.

SuperDuper clones user volumes but not Lion Recovery partition (and others).

If you really erased the raw hard drive (initialize, which is normally what people do in Disk Utility before restoring a clone) then it wipes out Lion setup.

A "clean install" of Lion will setup a hard drive, and then you can use SuperDuper to restore to the HFS volume alone.

You and I would hope and think Disk Utilty might or could be smarter than that!

If you hold down "command-r" on startup on a proper Lion install with recovery (recovery partition can be on an external drive instead, but you would need to also do a CLEAN INSTALL of LION), then it would use the external drive.

Using Option (Alt) will also show this "hidden" recovery partition.

There are other such partitions. GPT 200MB that controls the hard drive and BCA makes into hybred (turns the MBR holder into an active slice for Windows to use, otherwise there is just a protective MBR to prevent foreign OS from abusing the drive).

There is an 128MB EFI for each HFS volume also.

Windows 7 normally has 100MB System partition that it creates when installed.

You won't have a Windows partition, yet.

Boot Camp Assistant creates a FAT32 "BOOTCAMP" partition. You aren't there yet. Read the FAQ and install guide, and How To. http://www.apple.com/support/bootcamp

It depends IF you want to maintain the Lion Recovery and where.

I would stick with SD.

Lion Recovery can be on any or all drives.

I got more into what you were seeing.

One tip, shrink the HFS volume you restored, or shrink first, then restore.

Leaving 14GB of free space. Do Boot Camp Assistant and install Windows, then resize to reclaim.

Could even set the free space to be large enough for Windows, using Disk Utility to create/erase and then restore.

Not knowing exactly what steps and what actions, some of this might make more sense if you see and read what posted about Lion.

OS X Lion Install to Different Drive

OS X Lion Some features Lion are not supported during installation

OS X Lion Recovery Utility

OS X Lion Installer reports This disk cannot be used to start up your computer

OS X Lion About Lion Recovery

Managing Lion restore drive MacFixIt

Recovery options for Macs running OS X Lion MacFixIt - CNET Reviews

Lion and Boot Camp 4.0

And, some people found their Lion upgrade w/ Windows went better if they cloned 10.6.8 to another drive, did the upgrade to Lion there, then restored the upgrade back to their internal drive, leaving the existing partitions as is, and avoided trying to have Lion + Lion Recovery + Windows all on the same drive. I think both Lion 1.01 and Boot Camp Assistant 4.01 are a bit better now.

With a new hard drive, I would have done clean Lion install. And if you can or didn't, having Lion installer saved for future use and to reinstall is helpful.

How to prepare your Mac for OS X 10.7 Lion

How to keep Snow Leopard when upgrading to Lion

Install Lion on partitioned HD Apple Support Communities

How to create an OS X Lion installation disc

Unable to install Lion Recovery Partition Boot Camp

And about partitions.

Check partition table health in Lion's Disk Utility

Manage all partitions with Disk Utility in OS X