Jack is right!
Someone (maybe Jack and I, with help from others) really should make a recipe regarding what to do, at what time, and how to verify thread on T4 builds.
Ian Karr did it pretty well on basic rebuild but there isn't a "make sure to do this" list when you have this stuff apart that I am aware of.
If I had the cases apart there is NO WAY IN HELL that I wouldn't have case line bore, and jug register flatness addressed.
Sorry
@Chad911SC but you stated the machine shop checked and "Cleaned" the cases.
The first picture shows enough debris on the top of the case and the registers still dirty that I rate that cleaning job as "Not done. even first stage not correct".
I'll go through at least 3 cleaning stages.
First is mechanical in the parts washer.
This involves scrappers, razors, wire brushes and should leave the cases pretty clean, much more so than your pictures show...
At times I'd be using brass/stainless "tooth brushes" and be working under magnification as my 60-year-old eyes are getting weak. I have "jeweler's lens" up to 10X.
During this first stage I would use the glass trick to verify "how bad" my registers are.
I would still expect to have them machined!
After this initial cleaning I'd detail the case haves (both internal and external) cleaning up casting flash/irregularities.
I'd do the RMS drain mods. I'd look closely at all of the oil system parts, probably buy the Tangerine upgrade parts. I'd choose an oil pump that had O-rings between the pump body and the case.
I'd remove ALL of the pressed in plugs/oil channel block offs and clean all of the oil gallies with gun cleaning equipment. Some of the plugs are difficult to re-seal. Multiple threads on here about sealing issues would need to be investigated/addressed.
I'd use a thread "chaser" (not a tap!) on every threaded hole in the block. B12 and air to finish and then inspection under magnification. Threaded bolt holes would look "NEW" after completion.
Big air (175psi) and B12, WD/40 would be used liberally.
All of this happens BEFORE it goes to machine shop!
I'd want the case halves cleaned in a "hot water" rotisserie parts cleaner and then have machine work done. this is second stage cleaning.
After machined parts returned, I'd want to be in a "clean room" if possible. Doesn't have to be "laboratory" clean but cleaner than the open shop.
After all of my mockup builds (at least two) I'd do a final cleaning (3rd stage) with alcohol and air and then do then do final build. At this point I'd be ANAL about the cleanliness...
On an engine with an iron block, I'll also include a "caustic solution" stage during the first cleaning (cheap oven cleaner) and request a caustic solution "vatting" at the machine shop.
The machine shop commonly ask me "why the cleaning? Your stuffs already clean."
I still have them do it...
Now, in the OPs case he's already back together. His registers look a SHITLOAD better now. If he used a large enough piece of glass and kept it FLAT during lapping his registers SHOULD be better.
Did you VERIFY the flatness via the procedure I provided (Dykem or Sharpie)?
If you did, you're good.
If you didn't...
Now Chad gets to make a decision. Try it or back track
One other point, when I was actively pursuing a T4 build I found SO many rod lengths available that ending up with excessive deck was not going to be a problem.
It was the other way round for me. Pistons were far more likely to be sticking out of the jugs and this required metallic "shims" between the jugs and case. Thick ones!
I bought a set of extended length head studs because of this.
I AM surprised you ended up so far down the bore without reusing the stock rods.
This was part of the reason I got the initial deck adjustment WRONG. All of my computations for a T4 were to increase clearance, not reduce it...
Another thing I'd do automatically.
For ANY performance build nowadays.
Ceramic coating on piston crown, chamber, and exhaust port...