Hi,
Drop me an email i can send you the A4000T manual, its the Amiga Technolgoies manual but the Commodore board is almost identical minus differences in the case and release versions of the SCSI/AUDIO/IDE module boards.
I would be careful in using A1200 Workbench library as the A4000T has extra workbench disk which contains several additional files including a different workbench.library (i think its 40.70) which is not the same 'revision' as the A1200 ROM release.
If you have OS3.9 you can pull the files from that CD as it has everything you need.
It contains the install for OS3.1 as well on that CD.
The IDE port will only support 2x PIO-0 , personally I would only use the internal IDE for CDROM and use the SCSI bus for any Storage Media its much faster (talking from experience) but again thats my personal choice.
Be careful with VGA adaptors, ecspecially external flicker fixers as they run hot on these machines...
Get a GFX Card ASAP.. small vga adaptors should be fine
Also if you doing any kind of changes with the case off make sure that the power is unplugged and your earthed, you be surprised how quickly you can blow the board with static. ive done it once... so im letting you know be extra careful.