We have used Belzona 1111 for years to do in-frame block deck repairs on Cat engines. This is considered an approved repair procedure and has kept many engines running for years with many different types of damage (corrosion and/or cavitation pitting, general deck damage). It's a better version of JB weld. I suspect this would be an excellent application for this material. It would be easy to do a very successful repair without taking the engine out and apart using this method. The stuff is expensive and from what I can see only available in 1kg tubs, so Devcon may be a more viable option based on cost... but the repair procedure would be the same.
If it was me, I'd turn the engine over by hand to get the closest piston at TDC and then mask the area off and plug any and all ports/passages. In this case, those thread impressions would be a real asset for keying the liquid filler to the block. the surface just needs to be super clean and dry. I would control the total amount of the product used with a dam (putty, tape, etc) to stop the oozing off the edge of the deck and keep the material just above the deck during curing. A cast iron straight edge (or something else rigid and flat) with sand paper ( 150 to 180 grit IMHO) glued or 2 sided taped to it would be very workable for sanding the cured material and decking the whole surface. With a light touch it's not hard to maintain the flatness of the surface. After sanding, I would carefully turn the engine over to set the closest piston at BDC (bottom dead center) and then wipe out the bore with a clean lint free cloth. I'd then carefully blow the area off with compressed air and then do a final cleaning with brake clean or some other suitable degreaser.
My only caveat is that I would run the engine for 5-10 minutes after assembly and then dump the oil and filter while the oil is hot and any solids in suspension within the oil....