Personally i didn't have much issues with noise on TJ08-E, given that the case is not meant for quiet operation, you can achieve a pretty decent setup with it, the biggest problem is the frontal fan, which at stock (1200rpm) is very loud, even using the switch on the side to low setting (900rpm), still very noticeable, below 700rpm starts to become a wosh, and around 500rpm is pretty decent fan imo, i couldn't hear any clicking nor motor noise, still not dead silent as its beside a mesh, so air will still do a small wosh, but to me was good enough like that, user to user this varies.
With the motherboard, the GENE V is a sure nice motherboard, i had the GENE IV and GENE VI, the GENE IV had issues with fanXpert to be able to control the frontal fan, but the GENE VI is pretty good with FanXpert2, it manages to drop down the frontal fan to 470rpms where to me its very quiet. That said, i think the GENE V has FanXpert2 but im not sure if it will totally work like the one that comes with Asus AI SUITE III, my guess is it will be the same, but idk for sure, if its not be prepared to undervolt heavily the frontal fan. I also agree with comments above in terms if you can find a lower price Asus motherboard with FanXpert2 go for it.
HDDs, i never installed more than 1, i initially started with a Samsung 7200rpm 500gb (dont remember the model), the drive had a click on startup, this click was very loud and could be heard every time i started my PC, so the TJ08-E will not dampen much, but once it started, i could never hear the drive seeking or even writing, if there was a noise from it i couldn't hear it mounted on the bottom slot. In time i moved into a 2.5 Hitachi 7k1000 also 7200rpm that vibrates some, but very low noise seeking, i mounted on 3.5 no vibe that has a suspension, and i also couldn't hear anything on it, but all my mechanical hdds are only used for storage, no programs are installed on them, so there is barely any use on them. That said, i recommend you if you can to slowly start getting rid of the 4 hdds you own and go into 1, WD RED 3tb is a pretty solid drive, and the bottom cage will not interfere with coolers on the TJ08-E, you still have a bottom case ssd mount to have both at the same time. You can also suspend one or two hdds on the 5.25 on top if you are into that, i personally think buying a quiet enough hdd is good enough for the TJ08-E.
Now remember the TJ08-E even if its made of steel is not as solid as the 182, the side panels steel but a little thin compare to antec usual (not the 182 but others like solo ii, 1200, etc). Overall i still think its a fine, even SPCR gave it the Editors Choice on their review, SilverStone Temjin TJ08-E: MicroATX Evolved
, but its not a case to plan on it alone helping you deal with noisy components, chose careful and be prepared, and you should end up with a decently quiet setup. Another suggestion if you dont want to upgrade the hdds and willing to stay with 2, is to build on a SOLO II, it comes with hdd suspension so it should be pretty decent and you probably wont need to buy another motherboard.