My 2c might not be worth that much.., but I'll toss it in anyways, even though I have not been to that area in years. BTW: Many here have shared many good DIY ideas.., and my 2c may, or may not be worthy.., lol.
Your nicks actually gouge into the polished metal surface of the crank surface, hence often cratering it, i.e., pushing some material from the impact site outwards above the surrounding surface. Those raised edges of such cratering will scratch any metal in rotational contact, or in your case the mating surface of the two-halve RMSeals. Seems it is that expert advice is that you must replace the crank-shaft if you damage it during a RMS job, or have that area of the crank reduced in radius, and having a shim/sleeve installed. Hmmm..! But.., rather than scratches, I see only nicks. I would think deep scratches would readily allow oil to slip underneath the RMS, (in most cases).
However, I look at your pictures, and am of the opinion that the engine is outside the engine bay. I do not see a flywheel.., so I am a bit confused. If it is on an engine stand it would be easy to turn the engine upside down to more easily work on the problem area. I cannot picture myself having a good time of it working on my back on the floor, etc. My advice is to get a 4-point rolling engine stand. 3 point stands are a bad joke waiting to happen...
Anyways I would use a small tool, such as a narrow popsicle stick with just as a narrow longer length strip of emery cloth wrapped onto the stick, i.e., sandwiching the stick, (looped over the end). It will be tedious, and time consuming to lightly go back, and forth over the spot(s) in order to remove those raised micro-edges. After much satisfaction I'd repeat using crocus cloth. A magnifying glass, think; 'jewelers loop', would be handy to determine if you've gotten those raised edges removed. In addition a handy bladed feeler gauge could be used to slide back, and forth over the nicks to determine whether, or not, there are any raised edges remaining.
My thinking is to not damage your replacement RMS where it can be scored, (creating a groove, or two, or three, etc., all the way around both seal halves), by those metal edges cratered around those gouges you made.., but instead to remove those protruding edges firstly. Once done it is likely you will have haphazardly created a flat spot on, and around the gouge/nick/scratch which will be similar to a shallow 'pot-hole' which will allow oil to 'puddle' there-in, and spin the oil to the outside. Good chance that the seal will ride over said smoothed nicks, remain undamaged thusly minimizing oil leaks, (I'd live with that).., compared to seals that are grooved/damaged by scoring them by spinning over, and from those unattended raised metal edges.
Back in the day with my 258 cu. in. I'd just use red rtv, using the soap, and oil on the appropriate surfaces of the RMS halve requiring said, during installation. Easy job in those days, i.e., a lunch time job. Some like the black stuff you are inquiring about, some the copper, and some use the product called the 'right-stuff', blah, blah. Me.., I'd just ask the parts store clerk what the area mechanics use for the RMS rtv, and buy that. Use the phone if you live far away from a store, (since you seem to want to order some form of rtv via Amazon), in order to satisfy your need(s).
My emery, and crocus cloths do not have any inked stamp indicating the grit levels.., lol, they are what they are. Not exactly scientific factually, but I can tell you, as mentioned above that I'd use emery firstly, and crocus secondly. In the past I have used both cloths shoe-shinning my 258 crankshaft surfaces that had some grooves created by debris caught up between said, and a bad rod bearing, or two. In doing so I rotated crank, and or the positioning of the 'shinning' process in order to maintain roundness. On the engine stand I Installed rod(s) using plasti-gauge in order to ascertain that the replacement bearings were within proper limits.., in 4 places 90 degrees apart, and noted the averages in order to work into a constant round. (IT LIVES...). Yes it would have been perfect to send the crank out to have it turned, but...
Finally.., lol, there are some oil additive products that are often used to 'seal' up leaking RMS's. You never mentioned the year of your 4.0, but my '89 had a leaking RMS. Maybe a quarter ounce overnight, 1/4 quart of oil a week, i.e., (6 days of 50 mile trips). Got worse when I used synthetic oil. Switched back to dino oil, and some RMS stop leak stuff, and not much leaking anymore. Wanted to just replace the RMS, but the P.O. used that BLACK rtv between oil pan, and engine, and I just could not separate with propane torch, hammering, wedging tools, razor blades, blah, blah. Anyway I think the consensus is not to use synthetic engine oil in engines with old RMS's.
With that all said, (2c), I think you will get by.., by removing raised metal edges, replacing the new RMS properly, and using some RMS oil sealant stuff, and black.., hmmm..., not me. I'd just use RED, or maybe copper if I ever thought I'd be back down there someday in the future. Shoot.., you could just care--less, and use anything, sell the car.., and have someone get mad at you.
