Lion does best when you do a clean install on a new drive, then use Setup or Migration Assistants.
You're going to have to show / ask what old stuff you carried over from before most likely.
Then again, people complained when Snow Leopard came out. And before that there was...
To say it starts and shutdown more slowly is the surface superficial and doesn't say how installed, what, even the model Mac Pro and how it is configured.
You are going to want to use Safe Mode and Lion Recovery and backups for starters most likely.
reset SMC For "Mac wont' turn on or boot" and related
General purpose Mac troubleshooting guide: Isolating issues in Mac OS X
Creating a temporary user to isolate user-specific problems: Isolating an issue by using another user account
Identifying resource hogs and other tips: Using Activity Monitor to read System Memory and determine how much RAM is being used
Starting the computer in "safe mode": Mac OS X: What is Safe Boot, Safe Mode?
To identify potential hardware problems: Apple Hardware Test
General Mac maintenance: Tips to keep your Mac in top form