Yes, prolonged use of ibuprophen is linked to health problems such as bleeding stomach ulcers, gastritis, & even some heart issues. Are u alternating what muscle groups u work on every day? Like work upper body today, lower body tomorrow? If not, you're probably have some repetitive motion injuries by not letting ur muscles recouperate. You also need at least one day per week with no work out to allow ur body to rest. I reccomend that u trim down ur weight lifting to the point u were before u ramped it up. Then, start very slowly intensifying ur workout: week one add one rep to every set, week two add one pound of weight, week three add another rep, etc. This will help u slowly gain muscle safely. In the meantime, try icing ur sore muscles (15 minutes on, 15 minutes off) before going to bed. You can even alternate ice with a heating pad, or use a non-asprin sports cream.
BTW, it is tylenol, not ibuprofen, that causes liver problems.