Need help

I’ve been experiencing many problems with my 1992 and I don’t have the money to hire a mechanic. 1. Radiator fans won’t turn on unless I turn on the ac, if I do turn it on an awful grinding sound will be produced when mildly accelerating 2. The cooling system is absolutely filthy, my dad and I tried to clean it by removing the radiator cap and placing a hose over it and letting it run until the water is clear rather than a nasty chocolate color. When the car kept overheating we tried to flush the cooling system, we’ve tried 3 different flush products and flushed it 6-7 times and the result is still the same nasty chocolate like color. 3. At times I can’t shift into gear, sometimes while I’m driving I can’t put it into second or third while upshifting or downshifting. The last time I drove the car (2 days ago) I was at a stop sign and I couldn’t shift into first, second or reverse. In the mornings sometimes I can’t put it into reverse, to fix this I go into first and inch forward slightly then go into reverse. Shifting also feels rough sometimes like I’m scraping metal against metal. 4. When starting the car a small rattling sound can be heard for a second which disappears once I actually start driving, this sound becomes louder and more apparent when starting after stalling. While idling the car also makes another quieter grinding sound separate from the sound I mentioned earlier. The car can also idle roughly with the revs sitting around 500 while the clutch is fully depressed.

The only mod I’ve done is a short throw shifter, nothing has been done to engine, any advice is greatly appreciated