The pipe from the turbo over the rocker cover and into the inlet is part of the EGR system. Exhaust gas recirculation system. some of the exhaust gauses are recirculated back into the inlet to be burn in the engine again to meet various emission standards. If you have no emission requirements you can remove this pipe and blacnk off both ends in the turbo and inlet manifold. There are vacume controlled valves on the inlet manifold that control this operation, if they are faulty it may account for some loss in performance.
It's a 2.8L rodeo, I'm guessing it's a 4JB1-T and you are in Australia?

But it sounds like you have incorectly set the tappets, what did you set them to, and engine hot or cold? I don't have my book handy right now so can't help with that for now.

Other things to check are fuel filter and air filter, both can effect power if not maintained. I suggest and replace them if you don't know there condition.

Let us know how you get on, this is fixable.

Note; The time to alow for turbo wind down is mainly to let it cool down rather than spin down. Parts of the turbo are at exhaust temperatures so can burn up the bearings without oil and water flowing to cool down.