IIRC, the additional 4 signals are
41: +5v (logic)
42: +5v (motor)
43: GND
44: Type (0=ATA)
The pinouts you need are:
40 pin
http://www.cablingdirectory.com/pinouts/internal/ATA40PinCablePinout.htm
44 pin
http://www.cablingdirectory.com/pinouts/internal/ATA44PinCablePinout.htm
HOWEVER: please remember that the pinouts above are not numbered in the same order as the conductors in the ribbon. Due to the way the connector is constructed, the ribbon conductors alternate between top and bottom pins. In other words:
1 2 3 4 ... 20 21 22
| | | | \ | /
OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO
| | / | \
23 24 ... 42 43 44
1 2 3 4 ... 18 19 20
| | | | \ | /
OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO
| | / | \
21 22 ... 38 39 40
If you label each wire on a sheet of paper, you'll see that there is no simple way to directly connect the two connectors, because the ribbon layouts are very different. Besides, crimping ribbon connectors onto loose wires is a pain
The simplest adapters I've seen are PC boards with a 40 pin female connector, a 44 pin male header, and a HDD power connector for the +5 (red) and GND (black) wires. All the routing is done with traces.
The other remaining question is whether to use straight headers or right-angle headers. Right angle connectors offer a "edge-on" connection, which is easier to use in tight spots, but straight headers let the PCB lay flat on the motherboard. In many compact systems, there's no space to "stick up" (and if space wasn't tight, they wouldn't use a 2.5" HDD and 44-pin IDE)
