4L80E Might be missing a gear

[Mr-Jack]

So I have owned this truck for about 4 months. So far i've had to replace a few things but I'll get to that.

2001 2500HD CCLB 6.0 / 4L80E (4.10 gears).

When i first bought it, it had a 6" lift on 35" Toyo MTs.

Fealt a big rearend clunk when shifting out of first gear, so I figured it couldn't hurt to get a tranny flush. Got that done, clunk went away. Did new iridium plugs, 10.4mm Taylor wires, new intake, exhaust, and HPPIII tune. Shift points were adjusted as follows: 1-2 +3, 2-3 +2, 3-4 +1. Updated tire size, Eliminated rev limiter, and shift firmness is firm as well. Replaced fuel pump due to a bad check valve not keeping the line primed then just replaced a radiator that had a hole in it. Other than that truck runs pretty damn good for 140K+ miles

I had a feeling that it wasn't shifting into 4th. at around 45-50 mph it acts like it is going to shift but i don't feel nor hear it. at around 50 my RPM is 2400 which seems high. The online RPM calculator says my RPM is high, but not too sure. (this is the calculator i'm using http://www.csgnetwork.com/multirpmcalc.html)

I have started to notice this more now that i have an exhaust and can hear the truck shifting. Is there anything y'all can tell me to help diagnose if 1: i'm and idiot and it's shifting fine or 2: what is actually going on with the tranny.

I've never done much to auto transmissions before so i'm hoping someone else knows what's up.

Thanks in advance.

Jack