You say you let the car sit for awhile? You're checking the fluid level wth the engine running, right?

yes, but it shows full but it has significantly less than what came out.
plus it seems thats it not really an accurate measurement since there is a lot of splash up the dipstick, i dont really feel its accurate since 3.5 went in, 5.5 came out and now with less than before, it doesnt engage.

You posted previously:
Correct me if I'm wrong, but with the ATF level "correct", the vehicle engages R and D normally, and reaches 3,500 RPM @ 30MPH, but won't upshift?

Now, it won't even engage R or D, and the engine just revs??? This is getting confusing. Is the ATF level correct or not?

When the dipstick said overfilled but i replaced nearly as much as i removed, it engaged R and D but first only due to limp mode.
When I removed oil because dipstick said it was overfilled but it was the same I had removed in the drain process, it now doesnt engage R or D.

So it appears that the dipstick reading is incorrect or there is too much splash to read it well.

But how can it be full with only 3.5L when I removed 5.5L ?

I think you should add some ATF so that you can drive it to a nearby shop to have it checked out. Keep us posted.

After removing the valve body and not draining the torque convertor the trans should roughly take about 4 or 4.5 litres. Did you make sure the manual valve is lined up with shifter? It fits in a small groove on the drivers side of the valve body. This is easy to miss. also if the filter has fallen out if the hole in the valve body the pickup point for the fluid is now higher and will pick up air easier.

update:

I put in 5L of fluid, that which i removed and low and behold, it engages R and D (1st gear). i am taking it to a shop to have the codes pull and cleared and to get it out of limp mode. Will update you when I have the final answer.

Had computer cleared today, car is back to normal. Thanks for all the help.
Independent shop with Snap on with MB module was able to correct this.