Earlier this week the libby transmission started shifting funny from 2nd to 3rd gear, and from 3rd to 4th gear i believe, there is a short delay when shifting in those gears and you can feel it rock the suspension on the jeep, its not as noticeable once the trans warms up but still there, checked transmission fluid level while on a level surface with it in park when it was fully warmed up, and it was between the cold midway between cold and hot on the dipstick, is the level supposed to be between the two small holes towards the top of the dipstick were it says hot?

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05 CRD Limited, SEGR Kit, EHM, Selectrack Alpine DVD, 6000k HID headlights, Aux Lift Pump, 2.5" straight pipe, Diablo Extreme Puck, Euro converter
02 SLT Cummins H.O. 6spd manual with southbend 3850dd, fass 150hd, ddp 150hp injectors, arp studs, adrenaline stacked w smarty, traction bars, 6 inch stacks, level kit, bhaf

Section 7, page 744 of the factory service manual shows a temperature and level. If you don't have a owner's manual, they're hidden in a kaki green bag on a shelf at the top of the glove box, you can down load a FSM at the link given in Sam's CRD guide for NOOB's. It's a sticky near the top.

Basically at 180 degrees it shouold be at the top hole.

See the FSM

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Atlantic Blue 06 CRD Limited (his)
Joined by a 2000 XJ Classic (hers)

Depending on what version of the FSM you have the 545RFE automatic transmission dipstick reading chart is in the transmission Section 21 pg 225. Cold fluid (70 deg) should sit just above the "d" in "cold", much below that and you are low. Fully hot fluid (150-180) degree should sit between the lower and upper hot marks. Best to measure cold or fully hot as there is a curve involved in between (Note-rule of thumb on fully hot is the end of the stick and the fluid on it are extremely hot to the touch). Your symptoms sound like the low fluid symptoms I had with my Cummins D-250 when I blew the threads on a line fitting.

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Sold to LOST member my 05 Ltd, GDE Stg II turbo + TCM tune, SunCoast TC w. Transgo kit, Steiger window regulators, Samcos, Fumoto valve, 2nd gen filter head with Lub. Spec. bleeder, Hayden clutch & 11 blade fan, inverted spare, P-1 battery, BF Goodrich Long Trail TAs, Etecno1 glow plugs, timing belt at 50K miles/8 yrs