Liner? I thought it was called a wear sleeve?

Anyhow, it might very well be a case of "death by a thousand cuts." All of the aforementioned issues do affect performance (grooved/worn wear sleeve, dull/damaged impeller, bent intake grates), to what extent depends on the nature and significance of the damage. You might also have a look at the bottom of your hull, especially if you have a tunnel hull as dents and deformation can affect performance as well. I'd be willing to bet a new wear sleeve and straightened intake grate fins will sort you out.

The glacial silt in a lot of the rivers in AK does a number on both aluminum impellers and wear sleeves. If you put more than about 100 hours on your jet boat in silty rivers, you can expect aluminum impellers and wear sleeves to last about two seasons before performance very notably starts dropping off.