I'm not convinced that the head gasket is your problem. What does it look like. Sounds like there should be obvious damage to the gasket "fire ring". The reason I am dubious about the gasket is that CAT used the ferrules and rubber grommits on all the water passages through the deck of those engines. This should make it a lot easier for compression pressure to find it's way out to the outside instead of going into the cooling system. Most other designs use only the gasket, so if compression eats through the "fire ring" area of the gasket, then it is still contained by the gasket and finds the nearest low pressure outlet which is usually a coolant passage.
When you have the head checked, If there is some way to pressure check it, say by bolting a plate over the #1 valve/PC chamber area with a suitable gasket, and it passed that test with no leakage, I would feel a lot better about putting it back on with a new head gasket and grommits.
SJ, an old time CAT mechanic, who was on here for many years, always recommended brushing a sealant on the gasket of those long heads to avoid seepage along the gasket later. Avoid the fire ring area if you do this. Seems to me this will make it more likely to eventually get compression into the cooling system if the gasket ever fails, but it was done to prevent the all too common and ugly seepage down the side of the engine.
I have never seen the water directors be damaged in any way in the heads I have removed, but if they were eaten up by scale removing treatment or just corrosion, then they need replacing, taking careful note of which way the outlet points.
This page on liner protrusion is from a later series engine, but I think it is applicable to yours and I have never seen anything referring to the D318 as far as liner protrusion goes. I didn't have the nifty gauge when I did our D7 a while back, so I used a straightedge and feeler gauges to measure and large flat washers and pieces of pipe cut to take up the space on the studs and hold the liners down. Your liner should not be so apt to move around since it's been in the block for a long time already, but new ones do move down quite a bit when you tighten the hold down clamps.
D2-5J's, D6-9U's, D318 and D333 power units, 12E-99E grader, 922B & 944A wheel loaders, D330C generator set, DW20 water tanker and a bunch of Jersey cows to take care of in my spare time😄