Help me find the umph in my 360

Full throttle upshifts at 3800-4000 is because you have a truck trans. Needs a higher rpm governor. Try 5600-6000. Don't need to pull the trans to replace the governor - just the extension housing. A&A, among others, has a wide selection of governors.

50 mph at 3000 rpm is not right for 3.55 gears. I'm guessing your speedometer is wrong. I think I checked mine with GPS app on my cell phone. Again, if the speedo gear is what came with the truck trans, probably not right. The speedo gear can also be replaced with the trans in the car.

Not sure why the delay of manual shifts, but I'm thinking the truck valve body might have something to do with it. Shift kit??

I'd say it's certain you need a better torque converter.

Pistons .100 in the hole at TDC were not the best choice, but my 360 (short block dates back to 1990, when 360 piston choices were very limited) runs well with that same issue.