When you say issues, will it not run at all?
The engine running is needed anytime you pump anything through the raw water cooling. This is because the engine exhaust creates back pressure that both prevents water from entering the exhaust manifold as well as forces water up the riser pipe to exit the exhaust.
If you can't run the engine, your best option would be to disassemble thr feed to each component and blow it out with compressed air. That would include.
1.. the exhaust manifold.
2.. tha exhaust stand pipe.
3.. the intercooler.
You will also have to deal with the exhaust can, which always has some water in it. If it were me, I would just undo the clamps and take it out.