2001 Toyota Tacoma Transmission problems

I recently bought a 2001 Tacoma. When I bought it it already had 145,000 miles on it. After purchasing it I noticed that it shifted a little rough through 1st and 2nd gear when it was cold. After warming up though, the problem went away. Now, after about 6 months it seems to have gotten worse. I've noticed the shifting getting harder when it's cold and at about 40 to 45 mph the truck starts to vibrate. I've checked my transmission fluid and it's full but i've noticed it has a brownish color to it, would this cause the truck to vibrate like that at that speed?