You're hitting a few different points here.
Harmonics: crap crank with weak mains and psycho high compression and a mediocre HB. I’ve pushed 6,000 rpm using extreme measures and had the crank hold fine. The ultimate fix for all of it is p400, shy of that optimizer crank or scat crank and fluidampr balancer & Leroys billet pulley. In the fleets we saw many broken cranks and EVERY ONE had bad or highly questionable balancers. 100,000 MAXIMUM imo if the AC Delco or GEP (which may be AC Delco). 500,000 fluidampr
As for firing swap, gains are minimal on engines living at 4,000 rpm max so wasted $ imo on 6.5
The low power issue: they never figured to want over 220 hp or 500 torque even in concept. This is a fuel miser engine with low maintenance costs was the whole plan. Better power is available: big turbo,exhaust, pump/tune, cac, wmi, even if wanted propane works wonders in idi. Pick a target and have a realistic wallet to do it. Diesels are not gassers- no $250 power gains here.
Hot spots: were from coolant flow issues (especially amplified by rear head cooling kits), cheap metallurgy, and thin castings- basically 1 error and profiteering penny pinching. The optimizer fixed the metal and thickness. The spin on fanclutch/ balanced flow waterpump with restrictor fixes much of the overheating-with more help from better fanclutch. Then cheap radiator is the other part. Higher quality radiator with thermal coating to make up for undersized radiator and things can be happier. In fleets we ran hundreds and hundreds of trucks over 1/4 million miles and never suffered heat issues once set up right.
As for your cooling: Leroydiesel.com
What waterpump, fanclutch, fan, and since you have dual stat- what are you running as restrictor?