This is how my server will be laid out. The RAID trays have 40mm fans on them and the 5.25" drive bay fan has 3 40mm fans, so how would this work?
Do you think I'd have any issues with overheating, having 6 HDs?

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will your case take 120mm fans? if so use them instead as they move a lot more air. The raid cooling fans where are they going to get air from? it looks like they will just be circulating warm air around

No, just 90s & 80s, the raid trays pull air from vents at the front of the PC through the tray (and over the HD inside) and exhaust it into the PC tower

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ohk then so you have more air pulling than pulling out anyway of fitting another exhaust? perhaps modify the top of the case and add an 80mm to exhaust the air pulled in from the raid intake.

I think I could possibly have a 80mm fan on the side, there's a duct that would supposedly channel the air from my processor out but since I'm using a Slot 1 motherboard that wouldn't work. I might be able to remove that duct and put a fan in it's place, would that work to?
The only reason I'm against installing a fan on the top is because the keyboard will be sitting on top since I have no more room on my desk for another...
This is the case btw: Newegg.com - Linkworld 3230-02C2222U Black Steel ATX Mid Tower Computer Case 430W Power Supply - Computer Cases

Another thing I'm thinking is how effective will the slot fan, which is exhaust, be if it's right under the 90mm fan, would it be better to move it to the bottom slot, which is an ISA slot I won't be using?

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Thing to see is how hot it gets. Perhaps run it without the front inlet and see as the exhaust will then take the air away from over the raids

My only concern with that is that the HDs in the bottom racks will get hot, 4 together like that is a lot
The fan layout is similar to my main build, except the back fan is also 80mm and I only have 2 HDs, one of which is in a raid tray.
Speedfan reports the interior at 25c always, I haven't seen it change, but the HD & CPU temps change, generally from these variances:
HD1 (My main drive in an interior drive bay): 27 after it's been off for a while to maybe 38 at load, but I have a 50mm fan that blows air at it
HD2 (Backup drive, in a raid tray): anywhere from 33-38
CPU anywhere from 33-42
Not bad, but then again I don't have 6 hard drives in this computer....

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I hvae 5 hdds 3 optical drives and the cooling is all taken care of by a 120 mm inlet and a 120mm exhaust