Fairly long list to deal with here, because the information and request provides relatively little information.
It would be helpful if you could describe events and changes leading up to your machine's difficulty.
For instance: New hardware?, New programs or updates installed? First time the problem has appeared, or previous/random or regular events? Amount of Free Space on your Hard Drive? Recent large downloads?Programs and processes active at StartUp? sounds, smells, heat, noticed at time of problem? Sony Vaio may be a Desktop or a Laptop, which is it? How much RAM? Indexing Service on/off? Virtual Memory status? How many User Accounts? Primary use of machine (e.g. primarily a game machine?, primarily office utility and light web-browsing?, remote access to and from work network?)
Boot and Shutdown may occur for a huge number or reasons.
I'll take a few steps with you, but will definitely need more information to focus in on the problem.
Slow Boot and Shutdown may occur due to "nearly full" (less than 10% free space) hard drive, because opening and closing of applications and processes require quite a bit of space to temporarily accomplish read/write functions as the program is readied, or as the program product is saved and the program utility is put back into storage on the Hard Drive.
Slow Boot and Shutdown can be caused by Malware.
Even though you've got a clean McAfee scan, run some spyware scans and a few online scans:
Spybot Search & Destroy version 1.4
Housecall at www.housecall.trendmicro.com
Panda at www.pandasoftware.com/activescan
Ewido at
http://www.ewido.net/en/onlinescan/
Slow Boot and Shutdown can be caused by Missing or Corruped Operating System Files
Run your System File Checker
Start - Run - (type) sfc /scannow
(have your Windows installation CD handy for replacement of files as necessary
Slow Boot and Shutdown may be caused by various hardware failures including RAM, CPU and Power Supply.
Slow Boot and Shutdown may be caused by various corruption of Device Drivers.
Check in you Control Panel - System - Hardware - Device Manager for any yellow or red warnings.
Check your Event Viewer for Error information.
Here's a brief information article about using Event Viewer:
http://www.winxptutor.com/eventlog.htm
Please reply with information you may be able to gather by investigating the above lines of inquiry.
Best Regards