First off, building an engine is actually just an assembly process. Your local machine shop will take care of 99% of the critical dimensioning and finishing on the parts. Your job is to check their work with plasti-gage on the bearings, feeler gauge on the piston gap in the cylinders, straight edge on block and head surfaces, etc., then to do a very careful assembly job being sure you pre-lube everything with the proper assemble lube, torque all bolts to spec, make sure gaskets go on properly, etc. The machine shop will take care of 100% of the important head/valve work so you just need to tell them exactly what you want (for example, dead stock to factory specs or milled heads, bronze valve guides, custom springs, multi-angle seat, hardened exhaust inserts, etc.) then you just bolt them on.
Now about the 6 vs an 8. By all means go with the 6. I am putting this hopped up 235 in my '53 pickup;
These are marvelous engines and you can easily get 1hp/cu.in. with a little effort.
I highly recommend you do not use the '49 engine though. Prior to 1954, the 235 had several features that were not very attractive, including no oil pressure to the rod bearings, they got their lube from a 'splash' system. 1954 and later engines are totally 'modern' w/ hydraulic lifters, full oil pressure, etc. The easy way to tell them apart is the early 235 had the valve cover held on by two studs that go up through the valve cover whereas the later, desirable engine has 4 slotted screws around the rim of the valve cover.
Sounds like your engine may be junk. Water in the crank case usually ruins stuff quickly. Metal shavings in the oil is of lesser concern since the parts that were being shaved are likely bearings that will be replace in the rebuild. As long as the crank, block, and head, and hopefully connecting rods are in good shape, no problem. Your machine shop will do a detailed inspection of all the parts before they start working on them and give you an honest evaluation. Pistons, bearings, oil pump (new ones are pretty cheap), lifters, probably the cam, and misc expendable parts will be replaced.
In fact reportedly Toyota bought the casting patterns and molds from Chevy and built and installed the 235 in the Land Cruiser I think up into the 80s. As I understand, Toyota even left the Chevy casting markings on the foundry patterns! When I bought my '53, some previous owner had already dumped the original engine for a modern model. If you want to get really tricky and you can find one, Chevy also made a 261 and GMC trucks came with the same engine in displacements of 270 and even a 302!