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It could be other small rodents getting the seeds, such as mice or voles. These articles will help: https://www.gardeningknowhow.com/plant-problems/pests/animals/vole-control.htm, https://www.gardeningknowhow.com/plant-problems/pests/animals/garden-mouse-control.htm As for the plants wilting, this could be either too much fertilizer in the soil that is burning the roots or there are gaps in the soil around the plants that are preventing water from getting to the roots. Never put fertilizer directly in the holes when planting, and flood the area after planting to help collapse any air pockets around the roots.

Just plant them about 1/4 to 1/2 inch deep. Here is more information for growing cucumbers: https://www.gardeningknowhow.com/edible/vegetables/cucumber/tips-for-growing-cucumbers.htm

They may be damping off (which is cause by a fungus) or root rot if they were over watered. Make sure the drainage is good and add some fungicide to the soil to keep off the fungus. Here is more information on damping off: https://www.gardeningknowhow.com/garden-how-to/seeds/what-is-damping-off.htm

The most likely cause is leaf miners. Read more here: https://www.gardeningknowhow.com/plant-problems/pests/insects/leaf-miner-control.htm

Was the manure fresh or cured out? Fresh manure could burn the roots and cause issues like this, even death to the plants. You could try flushing the area with water to see if that helps. It could also be some type of fungal issue. Try treating the plants with neem oil.

It sounds like you may have bacterial wilt. This article will help: https://www.gardeningknowhow.com/edible/vegetables/cucumber/bacterial-wilt-cucumbers.htm