Based on your explanation, it seems like the filter is in the fuel pump itself. Is it that hard to take apart the fuel pump to access the filters.
Anyway, can a 01' fuel pump be installed on a 99'?
For 99/00 model, the fuel filter is located inside the tank. It is a white plastic thing like a column/stick with fine plastic filter.
The pump is located outside the tank while the later model has the pump inside the tank.
I've just had some stalling problem and was advised to check my fuel filter, fuel pump and fuel hose.
The hose is perfectly placed with wind-round wire and no kinking. The pump runs well, with the grrrrrr sound when the key is switch to ON.
So only the fuel filter left, it looks ok when I opened it with a little rust stuck there and here. The rust varies in size fine at the bottom and some coarse one.
But my tank was full at the time, what if the fuel level is low like when my stalling problem occurred. I drained the fuel and shake the tank with little fuel inside. Problem found! Lots and lots of rust, dark brown in color. The rust tends to saturate when the fuel level is low. So it clogged the column filter and that is why my bike stalls as if no fuel. Luckily the rust did not get pass the filter as the pump looks clean.
I will be riding tomorrow and report back if the problem solved.
Back to your q, no it wasn't hard to take out the filter but the tank have too be drained and taken off the bike.
01 fuel pump on 99? I'm not sure but I dont think so as they look totally different in design and in application but I'm not an expert