Enabling IDE on GA P35-DS3R

In BIOS under "Advanced Chipset/CMOS Features" there should be an "Onboard SATA/IDE Device" setting. Make sure it's Enabled.

Make sure your jumpers are configured correctly, check with only 1 device at a time if necessary.
As for flashing I've never had problems with the @BIOS tool just make sure you save the BIOS to a local disk first.
The BOOT floppy approach is safer but BIOS file corruption is more likely.

Thank you that seems to be the consensus, this build is the most complicated bios- vise. My others are so mickey mouse to this! Could I flash the bios from a usb flash in dos?

Q-Flash allows you to do just that, but the usbkey needs to have a FAT32/FAT16 file system. You use it by pressing the End key instead of Delete while on the POST screen. Be sure to check your motherboard manual for instructions.
(It's on page 66 for my GA-P35-DS3P).

Finally did it with floppy to F11. My two non raid sata2 seagates are
connected to the 2 orange connectors closest to the edge. My pioneer 112 ide is master with an ide HD in a removeable tray (mostly absent) is slave. Is this the issue should I connect them to the purple ones.
Is the southbridge fried? I am really confused.

The orange ports connect to the Southbridge (ICH9R).
The purple ports connect to the SATA/IDE device.
The southbridge doesn't have IDE.
You want IDE not SATA. So leave the SATA drives as they are.

Can you see the IDE devices in BIOS (Basic CMOS/BIOS Features) ?
If you can see one but not the other it's a drive issue (check power and/or data cables). If you can't see either it's either "disabled" in BIOS or dead but I doubt that it's damaged.

I just want the use the 2 IDE devices on that single connector. No I can not see the devices I can only see the 2 seagates on lines 1,3.(the other lines say none) I may upgrade to a sata based optical drive but have several IDE drives to use as slaves. I seen references online that some bios limit IDE detection time to boot faster and hence the mobo does not see the spin-up. Again this is an enhanced menu item.( I have read about CTRL F1 but how does it work key strokes and menu fields)

This is not a hidden menu item(you don't need CTRL+F1 to access it). It's under Advanced CMOS/BIOS Features (Onboard SATA/IDE device).
Check your motherboard manual if necessary.

If you can't see the IDE devices you likely didn't set up the jumpers on the drives correctly. Configure them for "single device" and test again. One device at a time.

If everything is configured correctly and you are sure you didn't misconfigure the jumpers you can take the board back to the shop/or RMA it and let them test it but as I said it's unlikely that it's broken.

Checklist :
Check jumpers, IDE cable, power cables ?
BIOS : Check Onboard SATA/IDE device is "enabled"
BIOS : Try autodetect feature for IDE drives.

CTRL+F1 gives you advanced menus for overclocking (you press it while on the primary BIOS screen, and then check M.I.T.).