I am setting up baritone to mine a perimeter but don't what to loose any blocks, is there any way to pause if the inventory is full so i can empty it and the to #resume?

You can try using a macro mod to automatically pause it or you can try using a mod to automatically throw out the items you don't need.
When writing java code is not a problem you can also add a process to take control and get rid of the items in some way, which I have done for myself (tailormade for a private 1.16.5 server and not meant to be used by others so likely not useful or useable for you).