Engine swap

R and L are from the driver's seat..... right?
Check the pumps again as to the heights of the drive flanges.

Did the trans linkages hook up OK?
You said the driveshaft fit, but is it all the way into the tail correctly?
Is the dipstick tube almost touching the firewall?
Was the accelerator cable long enough and not pulled nearly taut?
Did you have to rebend the trans cooler lines to fit?
Did the wiring harness fall into place?