1995 Honda Accord Not switching gears

Im having problems with my transmission with gears not wanting to grip or shift. Started having this problem a couple months ago, just haven't had the time or the money to fix it. Hoping its not that big of a problem and it's something I can work on at home. As soon as I start off, it takes a bit to get in gear (reverse has no problems). As its going through gear 1 to gear 2 it seems to go to a higher rpm than usual before it shifts to 2nd gear. But here is where my bigger problem lies, sometimes it shifts from 2nd to 3rd and sometimes it doesnt. It doesnt shift into 4th gear at all. Now my engine light is on as well. I just had my engine replaced about a year ago, but I rarely used my car because I had my '01 Civic to get around in. Since replacing my engine I've put in maybe 25,000 miles. A few buddies of mine said it might be the cylinoide, but I'd like to know exactly what it could be if possible.