Dude, you got money to burn or something? If so, let me send you my address so you can share the wealth!
Like dookie said, it only takes a little longer to do it right...but if you must completely revamp a design, here's a few pointers.
As Joe mama said, the easiest and safest way is to have a secondary controller card. The reason is to ensure that the drives involved have their own dedicated environment and direct paths to memory to avoid any sags or collisions in the stream.
Your controllers should also offer the highest throughput available. They should be UDMA133 capable, and have UDMA capable cables on them. Shoot for getting this support on your motherboard as well as the add-on controller. This way all your drives can be on dedicated channels and on seperate interfaces. In other words, have either the source or destination drive on a channel on the motherboard and the other on the PCI card. If you are using SCSI controllers, this would be a different story--you would want them both on the same controller because the SCSI will have it's own processor that will manage the transfers independantly of the CPU and motherboard chipset. But, who has the $$ to spend on 2 SCSI optical drives?
Speaking of drives, they do need to be FAST and RELIABLE drives--especially the reader. I have become very fond of the Hitachi designed readers because of the balance between price and performance. The Plextors are awesome readers if you've got the cash for them. I haven't had a chance to see their DVD burner in action yet, but the Plextor burners always got great marks on their CD burners. Both drives should be tweaked to their optimum speed--UDMA active and Bus Mastering enabled on the controller card.
In addition to making sure your drives have the largest onboard buffer as possible (NO LESS THAN 2MB on the burner, 512K on the reader), you will need to enable as much buffering in your software as possible---so you need a lot of memory. Don't go bargain basement here either. It needs to be a low CAS configuration with a high bandwidth. If DDR, Dual-Channel is schweet if your board supports it, otherwise no less than CAS2 PC2700 with heat spreaders so it can be overclocked. If using RDRAM, make sure you can use QuadSPeed Architecture for the highest throughput (400 vs 800 or 500 vs 1000). Go for 512MB or more if using an OS based on the NT kernels. IF you are going with Win98 or ME, stick to 512. There is actually some degradation in performance when you push these to 768MB. Yes W98 can be tricked out to support 768 and even 1024, but you have to give up some memory mapping for your AGP card, so success/fail depends heavily on the vid card and it's configuration.
On that note, your CPU and FSB should be tweaked out as well. This doesn't necessarily mean overclocking the CPU (although this is a nice touch for other reasons). But you do need to achieve the highest FSB at a 1:1 ratio for your memory. For example, you can run an Athlon XP at 1800 MHZ by going 164 X11 or 133 X 13.5. Obviously, you get better throughput at 164 X 11 because of the higher memory transfer. You need to watch your PCI bus speed though, some drives freak out if it goes over 40 MHz, so you may be limited to 160 on the FSB if this is the case.
As you see, it's a big pain in the arse to cover all the bases. It is just SOOOO much easier to image to drive first. Especially with the prices of hard drives these days. You could easily nab a new high speed drive and high speed PCI controller card to speed up the process of imaging and be done with it. That is what I did years ago and it is flawless. I rip at 4-8X on my Hitachi reader and burn back to my A04 in like 30 minutes to an hour, depending on the disks. DV9-DVD5 encodes usually only take about 1.5 hours tops on the longer ones (LOTR2T took about 1hr 40 minutes). You really don't save THAT much time on-the-fly as compared to the added expense to do so reliably. Even then , it is not guaranteed. What happens if your source gets a read error or fails DeCSS? You lose a blank DVD, and have to resort to imaging first, then burning anyway!
If it ain't broke don't try to fix it! But, hell if you can tweak that bastard just a little bit more....hehehe.