The omega 3 is fine. A mimimum therapeutic dose is 4000-6000mg. If you have arthritis then it's higher ie 9000mg.
You're not getting a overdose as long as the vitamins you are taking are single dose ones (which all those can be). It's more an issue if you get a mix where you can double up with your dosages.
The 1000IU of Vit D is a standard dose for a deficiency. You probably want to get a blood test in about 2-3 months to see what your levels have done. If they've increased then you may be able to stop taking them but you'll have to watch your levels so they don't drop again.
Do you get out in the sun much? If you do and you still have a vit D deficiency then it's possible that you also have a magnesium deficiency. Magnesium is needed to convert sunlight to the active vit D form.
With the B12 - I'm surprised you aren't on the 1000mcg one. You'll need to check you blood levels after a few weeks. If your B12 levels aren't going up you may have a deficiency of intrinsic factor in your gut. If that's the case you will need B12 injections.
Your doctors have prescribed the expected dose for deficiencies. I'd be listening to them.
I don't know what the safe dose would be. But, I think you are taking too much, too. I would cut it in half or cut a few out completely. Just one of those efas would be enough. Except the Vit D, if you are deficient, you need the 1,000 mg a day.
It sounds like you are taking WAY too much omega-3!!!! Most doctors don't recommend even taking supplements because it can be extremely dangerous. It is very easy to take too much.
An omega-3 overdose is likely to cause any of the usual omega-3 side effects, but perhaps more severely. In particular, stomach upset can be expected. In serious cases, an overdose could increase the risk of bleeding, including dangerous internal bleeding, such as gastrointestinal bleeding or bleeding in the brain. Symptoms of such bleeding may include:
Easy bruising or bleeding
Black, tarry stools; bright red blood in the stool; or vomiting of blood (signs of gastrointestinal bleeding)
Signs of a hemorrhagic stroke (bleeding in the brain), such as vision or speech changes, weakness or numbness in an arm or leg, or a severe headache.
I took that from a website that I just found. It also says if you think you may have had an overdose of omega-3 then seek medical attention immediately. Please be careful. Wish you the best!