You will not be able to use all 40 GB as one partition under NT 4.0.
According to Microsoft: "The only disk services available to the Boot Sector code at this stage of system boot up are provided by the BIOS INT 13 interface...... This limits the size of the system partition to 7.8 gigabytes regardless of which file system is used. "
See the following URL for the details:
http://support.microsoft.com/support/kb/articles/Q114/8/41.asp
Note that Microsoft refers to the partition containing the boot files like NTLDR and NTDETECT.COM as the "system" partition. The "boot" partition is the partition with \WINNT and all the rest of the operating system files.
If you want to create partitions on the hard disk that are larger than the limits of 2 GB for FAT16 and 4 GB for NTFS on installation, you can install the drive as a secondary in a running NT system, then use Disk Administrator to create the partitions on the blank drive. Then transfer the drive to the new system as the primary drive and install NT on it into the existing partitions.
If you want to use the "whole" 40 GB as one big drive, here's a compromise.
When you install the 40 GB drive as a secondary, create 2 primary partitions as follows:
1) Partition #1 is FAT16. It is very small, a few MB (10 MB should be plenty). It is marked Active.
2) Partition #2 is NTFS. It takes up the rest of the drive (about 40GB).
Now when you put this drive in the new system and install NT on it, install NT to the big NTFS partition. Since the "system" partition is the small partition, it will still boot and you wind up with a system that has all your OS files and applications in one large NTFS partition.
JS