High RPMs after trans swap

I have a 1994 Mighty Max Macro Cab Sport. I engine swapped it a while ago to a 1990 4G64 2.4L. The 1994 Auto R4AC1 is stock to the truck. It has a center bearing driveshaft and stock 3.90 gear. I changed it over from it's slushbox dying trans and flex plate bluetooth itself from the crank LoL. It has been a month of sourcing parts and another month of weekends pulling out the trans and all. I replaced the rear seal on the engine. Rebuilt the manual trans center bearing driveshaft. Sourced a 90-92 6 bolt flywheel with bolts. New clutch pack. Put in my Wilwood pull style hydraulic clutch master and slave cylinder. Cut the square out of the floor for the shifter and cut a X in the carpet to get the shifter up in place. Found the wires for the Neutral safety switch and reverse lights off the stock harness and grounded the neutral wire for now. Swapped out to a manual trans steering column and manual trans pedal set (Gas, Brake & Clutch pedals). I had to be creative on the mounting of the slave cylinder and master cylinder mounts and connecting hardware.

Well finally getting to my question I drove it all day on Sunday and bedded in the clutch nicely and some fine tweaking and drives and shifts great. My RPM gauge is reading way higher than it should be at 60 MPH it reading 3,000 RPMs it never did that before with the automatic transmission. I took out the small under the dash automatic transmission computer but would my main ECU/ECM that sits in the passenger side kick panel would it need to be changed out as well to a manual engine ECU/ECM by chance?

Sorry the Manual Transmission is 1995 5 Speed R5M21. The engine isn't running at those high RPMs either.

its because the rear end gearing... its geared for the auto (which I believe is only 3 speed with over drive) and the manual is is 5 speed..

if you will be doing alot of hiway driving I would suggest swapping out the center section of the rearend to diff gear ratio..

do a lil research on rear end gearing on google and you will see (some pages with pics/videos.. what im speaking about.

hope this helps and good job on the swap sounds like it went well other than the high rpm's

I don't think so but could be. I do have a 3.55 gear ratio center chunk out of a 1986 1st gen D50 I was going to swap over anyhow. Most 2nd Gen trucks came with a 3.90 gear regardless if Auto or Manual. My 1995 2.4L 5 Speed Mighty Max has a 3.90 Gear in it also. I'll look into it though.
Thank You Man. I appreciate it.