1. Generally, no, but there are install issues reported for those with existing bootcamp partitions.
2. No, there is no such thing as a partition inside of a partition. It will be an additional partition.
3. Just put a copy of the installer on your external drive and keep a copy on your external drive in a location outside of the application folder. A DVD installer will be extremely slow.
It's much easier to to use Setup Assistant at the end of an OS install than to use Migration Assistant or to copy data after the fact. IMHO
I believe this article answers most of your questions.
You will most likely run into the error message that "Some features of Mac OS X Lion are not supported for the disk" if you have multiple partitions set up, especially if they were not set up using Bootcamp and/or have serveral different file systems.
You can confirm that the Recovery Partition will not be installed by checking Disk Utility for your current partition map scheme.
This is most definitely not the end of the world as it is quite easy to create an external Recovery disk.
1) No, you shouldn't have issues running Lion, but Recovery HD will not be created.
2) No, and in your case it doesn't sound like it will be installed on your internal drive at all.
3) Yes. If you begin with an empty partition, then install Lion that would be considered a clean install.
Hope that helps.