"Right way" is very subjective but imho it means to bring everything up to similar standards and of similar lifespan capability and having similar overall durability. So in that respect, despite that stock shortblock having lower miles, it will not be anything close to extra long lived with the inductions higher power capability and may suffer over the longterm with those now much higher cylinder pressures. Have to remember that engines weren't built to all that tight a tolerance, and even if you got a "good one" those tolerances were not all that long lasting, and the materials used in some of the components were barely above chicom parts quality and standards being sold today. This is why blueprinting used to be so popular on all the old factory stuff. The pistons are low compression brittle junk for any performance oriented build imo. Rattle them with preignition or detonation due to bad gas tune or maintenance related issues and they will not be much longer for this world. On the other hand, short stroke 289/302's are notorious for having excellent bore and generally decent shortblock life so long as they were not severely beat on, overheated, or never maintained properly. For anything performance oriented the rod bolts sucked eggs if you like to rev em' but new sets of improved OEM style stuff is about a 100 bucks these days. Which wouldn't hurt that bottom ends ability to meet your power goals and live a good long life. What you could do is stick with your original plan and run what you got with a fresh topend for now. Then plan to get a milder stroker kit to freshen it up later on. Probably need to go through the heads and freshen them up too at that point. It's a perpetual snowball effect but it definitely helps to have a well thought out plan. Another option. Pull the shortblock down, clean it up inspect everything(cranks, rods, pistons/wrist pins, all bearings including cam, and reuse what you can. Keep everything in precise order and mated to the locations it has been run in and worn against. Then use a 180 grit ball hone(also known as a dingleberry hone) mounted on a hand drill to refresh the cylinder wall crosshatch, put a fresh set of rings in it(I prefer total seals maxseal gapless stuff), fresh bearings, gaskets and run the bejesus out of it till you get bitten by the next powerbug. Not trying to confuse you here or send you down the proverbial rabbit hole.. just giving a few more options and perspectives.
