1. EGR - yu can try cleaning it but its better to just change it after doing all that work. Theyre not designed to be cleaned.
2. Remove either hose is fine, just put the bucket where the fluid comes out. Drain about 1 quart or two, reattach hose, top up ATF at dipstick hole. Repeat til its fairly clean. Youd probably use at least two gallons for this, is you are using Toyota T IV it will get expensive ($4- 5 qt) but cheaper than a rebuild i guess.
2. Remove either hose is fine, just put the bucket where the fluid comes out. Drain about 1 quart or two, reattach hose, top up ATF at dipstick hole. Repeat til its fairly clean. Youd probably use at least two gallons for this, is you are using Toyota T IV it will get expensive ($4- 5 qt) but cheaper than a rebuild i guess.