Sophia here from Shopify. Welcome to the Shopify Community!
Apps like Infinite Options or Bold Product Options will allow you to add more than 3 options per product. These two are paid options that I've heard other merchants have had success with, and they each offer a free trial. There are apps with free plans as well, so you may want to test a few to find out which will work best for your business.
As for the special message, the product options apps can help with this too. The other option is to ask your customers to enter their special message in the order notes section of the cart page. This is an easy, built-in option that will work well if there's only one custom product per order, though it may be more intuitive for customers to enter the message directly on the product page.
Can you tell me a bit about the products you're selling and the options they'll have? I'd love to take a look at an example (either of your own products or of another store you'd like to emulate) so I can get a better understanding of what you need and make sure I'm offering the best recommendations.