A 3 cylinders perkins (400 series) generator injector pump was removed without setting the timing. putting the injector back, the engine have miss timing. After several trials, engine cannot starts. How do I do timing since the timing mark on the gear did not work.

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Any engine runs better doing what its built for, but it should not be very noticeable. If you are familiar with this engine, then I would tend to go with your instincts. The injector timing is a likely cause and could be supplying more fuel than you need creating a laboured combustion which evens out under load.
Perkins parts were found everyware around western Australia 20 years ago and were cheap, I'm a bit out of touch on that aspect these days, but they are worth the effort, you should try to find some old school farmers around to speak with, they often have golden and unique solutions.

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Pump

Check the fuel solenoid is getting power. It may be locked out by loow lube oil pressure and other things.

ALSO when restarting a diesel one OFTEN must "bleed" the fuel lines at each injector... same as when one inadvertently runs a diesel out of fuel. Crack the connectors at the injectors and crank till fuel comes out and tighten each one. Yes, it is a pain...

If the unit has a battery box, measure it and get the largest size that will fit and of course the correct voltage. Diesels take a lot to crank.

You can search battery sizes on the internet for physical size. NAPA has a pretty good selection.

Low frequency means the RPM of the motor has fallen off.

Check your fuel is NOT contaminated or fuel filters plugged.

Further tests should focus on the govenor system. Possibly it fails when engine gets hot. the frequency is directly proportional to the engine speed.

I take it it's diesel. Have you renewed filters? Bleed fuel system Make sure there is plenty of diesel flowing out of tank (pipe not blocked) Check lift pump working

If we're talking about the thing that has a pipe to each of the cylinders on your engine then the answer is Yes, your injector pump must be correctly timed in order for the engine to run properly. This is the part of the diesel that does what a distributor on regular car engine does, namely ignition timing.

The exact procedure for setting the timing depends on what model of engine you have, get a manual from Perkins to be sure.

That said it usually goes like this:
1 - make sure the engine has the correct cylinder at TDC, this makes the gear connected to the camshaft be in the correct position.

2 - Set the pump at the correct position, this will either involve looking at a mark in a window on the pump (standyne pumps), or looking at the keyway in the shaft of the pump, etc.

3 - Bolt the pump into place on the engine making sure the gears/drive meshes nicely. Connect all the fuel lines to the pump.

4 - purge the injectors by loosening each fuel line at the cylinder end and cranking the engine until fuel comes out of the pipe, then tighten it back up.

5 - Crank the engine and start it, check the rpm.

Rank this answer if it helped,
Carl