Do yourself a favor and start with getting the injectors cleaned and while the injectors are out, have the engine's
compression and leak-down checked, that will give you an idea about the condition of the engine. If
compression is good, then just clean your
fuel system and have a competent tech check your
injector pump pressure and timing. I would also go through your
cooling system, whether
raw water or heat-exchanger. If
raw water, pull the thermostat,
water pump impeller, reassemble, connect an outlet hose that goes
overboard, and connect the inlet to a garden hose with an adapter that you can clamp on. You might even flush the engine in reverse, but I would bypass the
transmission part of the
cooling circuit. And while the
water pressure is on, open the cylinder cocks one at a time if you have them. Pulling the thermostat and
pump impeller should allow for maximum
water flush flow, and you should probably replace those items anyway. If you find you have low compression, or too fast of a leak-down, start with a valve job, and while the heads are off, check the cylinder bores for wear, if they show wear, or worse, vertical gouges, you need new cylinders, or liners, rings and most likely pistons...and a decent machine shop that can either bore and line, or just press in cylinder new liners.
You might be able to get away with new piston rings and honing the cylinder bores; make sure that you follow/check gapping recommendations for the rings, again, machine shop work.
And if you have to go that far, you might as well check the play on the bearings on the connecting rods. If they rock even a fraction, side to side or up and down (not slide, but "rock"), then you'll be pulling the block and you might as well do main bearings as well. A knowledgabe machune shop will be able to mic your crankshaft and let you know if you can get away with just standard bearings, or if the shaft needs grinding to undersize, and getting undersized bearings; but of course you'll want to find out if under-sized bearings are even availabe for your engine.
Lots of wrenching with this type of
project, but not impossible if you have the shop manual and a competent machine shop working with you.