So last week I pulled my tranny and threw in oem clutch, flywheel, pilot, and throwout bearings. Buttoned everything up except the VSS (hooked up wrong) and drove the suggested 500 miles afterwards. A CEL was thrown (I was guessing due to the VSS being hooked up wrong and my speedo not working) and I blew it off until a couple days ago. So I've started to run the car harder as usual (100% stock, 100% oem 1995 GSR) and something funky happened. After a hard pull up onramps I settle in 5th gear and cruise around 75 in the fast lane, both instances ( has happened twice now) my car goes into what seems as a limp mode, like if my relay had shut off. The first time I downshifted in to 4th after putting it into neutral for about 5 seconds and the car drove off like nothing happened. The second time I shifted directly into 4th and the car has no response again like a fuel related issue. After working my way across two lanes and slowing down to around 60-65 the car gets fuel again and drives off as normal. There are two things that I must note, first is that when pulling the tranny the we accidently pulled the wires from the 02 sensor (I believe, end going into the harness) the guy helping me did a little research and put them back in there supposedly the correct way. The second is that it feels like the car is sluggish in vtec. For some reason it feels like vtec is engaging odly, like in stages. It pulls hard from 4.4k to around 6.5 then feels like it hits a wall before hitting around 6.7 to redline. I've heard the knock sensor could send it into a limp mode, and a main relay, but I'm also crossed on if the 02 sensor is reading incorrectly, and why wouldn't it have thrown it before a couple days ago. What are some other suggestions, will probably pull codes here in a couple days. I appreciate the help, thanks.

 

if the speedo isn't hooked up, it will give you problems. the pcm uses readings from the speedo for operation of vtec among other things.
if the speedo hasn't been installed yet, do that. then check the codes to see if the o2 is wired correctly