You can certainly can overfeed pond fish. Its one of the biggest mistakes to make. Checkout the Ammonia section at http://www.gardenfishpond.co.uk/maintaining.htm . This describes what happends to the food that is not eaten. It may be worth buying a water testing kit.
Ive had the same problem in my pond. The best thing to do is to put the pump on a brick and put the brick in some type of roofless box like you suggest. This is the best combination as you only get small collection of sluge at the bottom of the box and as you have raised the pump slightly it should not get clog up that quickly. When it does lift the box out and clean it and the pump filter.
My pond at the moment needs a good clean. If I dont use this method I have to unblock the filter about once a day. Thats a problem to me and often I have to switch the pump off at night. Using the box / brick idea the pump will last about 5 days before it needs a clean. Hope this helps. I will add this to my website http://www.gardenfishpond.co.uk
In my opinion PVC offers the best choice because its better value for money than Butyl rubber and I am led to believe that its alot easier to install. I have written an a artical on my web site http://www.gardenfishpond.co.uk about the two types of flexible liners. Its been a while since I created a new pond and therefore if my facts are incorrect then please all let me know.
The main advantage of a flexible liner is that will adapt to any shape or size that you decide to make. There are two main types :-
Butyl Rubber - This will last the longest ( 30 years or more ) as it will not get damaged by the suns ultra violet rays. It is the strongest type of liner and therefore it is far less likely to get damaged by frost or accidental damage. For this reason it is slightly harder to install because its harder to bend and fold unlike the next type :-
PVC - This is the choice of most people, especially beginners as it’s the cheapest but will still last in excess of 10 - 15 years. The liners are normally sold with a lifetime guarantee in years of how long it will last. PVC is still relatively strong and wont be damaged by frost, but more care is needed to ensures that it doesn't rip or tear. It is more important to line the bottom and sides of the pond more thoroughly with this type of liner. The main problem with PVC is that it will eventually dry and split where its above the water line and in contact the suns ultra violet rays. By designing a pond correctly you will limit daily access to the sun. One of the best and simplest tips is to limit the amount of liner visible above the water line by simply checking that all sides of the pond are level. If you decide to edge your pond with decorative stones you can position them to overhang the pond slightly to create some well needed shade. Flexible liners are sold by rectangular size. It is important that the liner you buy will be large enough for the size of your pond that you dig. To calculate the size for any type of flexible liner follow these simple steps or use the calculating pond liner tool