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For ATF, go with a DEXRON 3 type fluid, or a DEX/MERC fluid. Stay FAR away from anything that says DEX VI on it as your seals in your 99 trans will not be compatible with it. Drain the pan, drop it, change the filter out, then put it back together with fresh fluid. As to your rear end, it should be a DANA 80 if you have an actual 3500HD. A diff cover isn't a bad idea, but not needed. As to fluid, 80W90 is what they call for, but you can run 85W140 if you want to. 75W140 is another good fluid to run. A bit on the pricier side, but it is very good stuff. It has all the benefits of 75W90 fluid when cold, as well as all the benefits of 85W140 when hot. As to amounts, I'm not 100% certain, but I believe the trans will be around 6-9 quarts depending on how long you let it sit and drain, and which pan it has on it(GM used both deep and shallow pans on the 4L80E). Rear diff should be between 3-4 quarts, and you will probably need a bottle of posi slip additive for it because DANA used clutch type posi diffs if it has one in it.