1997 Chevy Cavalier Grinding after put into gear

1997 Cav 2.2 5-speed. I noticed a few months ago during heavy traffic that there was some type of grinding after I'd put it in 1st gear but as I would accelerate it would leave as quickly as it came but that same noise would cycle back when upshifting to 2nd. Now, only 1st & 2nd were affected but as time when on it eventually worked it's way into 3rd and recently affected 4th. I had the clutch done 2 months ago thinking the grinding would be no more but it just keeps getting worse. FYI, about 3-4 months ago I nearly physically beat myself up for not paying attention 2 the manual transaxle fluid. So, when I was able 2 fill w/ fluid from dealer, the little dipstick on the tranny could not even read any fluid for fact that it had gone drastically low. If memory serves me right, this grinding arose a little before this fluid incident. Please help. No one else seems 2 know what's going on. Thank you greatly!