Hi,
1) "when I add an item to the cart and then click on continue shopping it stays on the cart page"
I just tried it and I cannot see the problem, ie, the continue shopping link successfully returned me to the home page.
2) "Will I be able to bundle ID #'s 9,22,45,89 into one sale at a discounted price?"
In short no. But you can use some of the options such as the quantity based conditions in the coupon settings to achieve a similar result.
3) "Can I apply a discount buy 3 get 1 Free?"
You can use the quantity option in the coupon settings to achieve something similar, eg,
Apply x% discount when:
"Total Quantity" -> "Contains" -> "3"
4) "Can I set up a % discount buy 2 or more and receive 25% off?"
Yes. Similar to above - use the conditional options in the coupons settings page.
5) "Can all these be integrated with affiliates and there payouts?"
Any sale of a product can be integrated with the Affiliate platform and the amount of commission paid can be specified on a per product basis.