Honda CRF 250 L Rally ABS
 

Recently, when the fuel level goes below 1/4 of the tank the engine starts to work erratic. Feels like engine frequently stops working for split second jerking me forward every time. I took fuel pump assembly out but don't see any obvious problems. Could it be that the filter is dirty? For last 6 months I was riding in Africa where the petrol is not good quality.

Very good guess and relatively easy maintenance item. Most FI systems also have a second filter in the injector body. You can access it by removing and opening up the injector body. Considering what kind of fuel you had, it's another idea to consider after replacing the main filter.

You can also have issues with a dirty injector (it can be cleaned by a specialist) or low fuel pump pressure (have a shop measure pressure).

I assume you are using a new tank of gas, eliminitating bad gas.

If there is water in your tank it will sit at the bottom as it is lighter than petrol.

However, if you've removed your fuel pump I would imagine you've already drained your tank.

Check that your tank is venting correctly too.

I've just installed a new fuel filter and the problem is solved.