If I have 3,000 logs in my bank, is there any way to put all of them in..

Yes, this is quite simple, actually. The way to withdraw more than 28 items at a time is to select the "Withdraw as note" feature in the bank interface, which allows you to withdraw all of the item from your bank while only taking up one inventory space.

Yes there is. On the bottom of your bank, next to where it tells you how many spaces you have left, there is a little icon in the shape of a note. Click that note and you will be able to withdraw all your logs as a notes. Click the note button again when you want to withdraw them as a regular item. You can only withdraw items as a note when they will take up more then one spot on your inventory. For example you can't withdraw runes as notes. Once somehting is withdrawn as a note, you can only convert them back at the bank and they cannot be used while in note form. They can only be traded or sold.