One last questions and I think we are very good to go.
Because we are using the index table, we have it setup to cron everyday, and re-index the added products.
At the time for which this happens our server hangs (approximately 5:30 to 6pm CST) until it is reboot. I have noticed this over a 4-5 day period.. We have checked error logs, and performance analytics and it seems to tax the SQL processes quite a bit, but I never have any problems with it during a manual build of the index. The only way I was able to reference it to the index cron job is by turning the process off and waiting for the day to roll over at which point everything is fine, and we are now on day 4 with no issues.
Hope that makes sense. Happy holidays!