kinkyintegra

Okay so i have an em1 and i swapped in a d16y8 from a 98 ex because my b16 is in the shop. well anyways....Ever since i got this swap I have had 4 CEL's....O2 sensor which is an easy fix for me, speed sensor which is plugged in but since my speedometer doesnt work i guess its broken, CFK sensor, and crank sensor....The reason the crank sensor is not plugged in because my harness is different than the obd2a plugs on the engine.
Okay the problem: when cruising in 4th or 5th gear on the highway if i stay in a certain rpm it feels like the tranny pops out of gear but it really is still in gear and when i downshift the car slows down and the rpms raise but no power gets to the wheels and usually i have to downshift a couple gears for it to catch. I just changed my tranny fluid to synchromesh modified, changed my oil and checked over a few things but I have no clue why this is happening. Maybe because the speed sensor is broken and it thinks it hits the speed limiter? Someone please help. Oh and i checked to see if my clutch slips by doing the thing with the ebrake up and putting it in 5th gear and letting go of the clutch and it stalled.