I am a bit confused with the detailed explanation. However, we do have a couple of apps on the Shopify app store that might suit your needs.
1. Simile Bundle
2. Simile Upsell
3. Simile Personalization suite.
You can find them here.
These 3 apps provide product pop-ups for adding to cart items in different touchpoints in different processes.
Cheers and hope this helps!
Let me recommend you KAD Upsell & Cross Sell. In our App you will have an option to create the required number of the offers with all the combinations that you need.
Pop-up or modal banner is fully customize so you can make it perfect for you store theme.
Here is link to the app listing: https://apps.shopify.com/kad-upsell
Let me know what you think about this. User feedback is highly appreciated.
Hope you are doing well.
I guess this in-cart upsell app will definitely help you. It has many upsell options.
And the Discounted bundle (product bundle) will look as follows: