To me, it looks like there is not enough clearance - not exactly sure why. You should get a good quality 2" to 3" barrel mic and measure all the journals . . . and report back to us the precise numbers.
On the main bores, a three-point bore gauge is the way to go, but unless you know somebody who has one, they are super expensive (for one that I would trust - like a Starrett). Also, you need to know that it is correctly calibrated - and know how to use it. The ones I use cost over $1000 . . . not cheap, but necessary.
As noted, there can also be a line bore issue - which is hard to check unless you have a precision rule that is 24" in length . . . and are used to doing it. The machine shop should have checked the mains - if not, maybe have them do so.
As noted by some, I use ScotchBrite on my flathead bearings - with a bit of solvent. I polish all sides of the bearings. I do not attempt to remove material to "fit" the mains, more along the line of just polishing them a bit. If the crank doesn't easily turn, there is an issue - which shouldn't be solved with Scotchbrite.
Are you sure you have the correct bearings for this engine and crank?
Once you get to the full-floater rod bearings, you'll need to first mic everything to figure out the clearances. You'll need a 1" barrel mic and something like a piston pin to measure the bearing shell thickness (I use a .750 flathead piston pin - then I do the simple math). You'll also need a precision bore gauge to measure the rod-bore diameter - or have your machine shop give you the numbers (which should be the stock spec). This will tell you if you're in the ball park. Then, you'll need to use a rubber mallet to "tune" their roundness to get them spot on. Also, you'll need to Scotchbrite them on all sides. The process usually takes me about 4 hours to get things exactly right - and I'm not a newbie (so plan accordingly). Also, I frequently have 6 sets of rod bearings and find the "best 4" to work with - as manufacturing differences do exist.
Here is a little video I put together last year that describes some of the process for full-floaters - hopefully you'll find some value in it:
https://www.youtube.com/watch?v=CyVLsPdbhS8
Best of luck!
B&S