Cannot see optical drive or read files from superdrive

This is my first ever posting so I apologize if I’m giving too much info.
A couple years ago I installed a Pioneer DVD-RW DVR 107D in the top bay of my G4 (mirrored doors) and put the combo drive (Philips CDD5105) in the bottom bay. Back then I was running OS 9. All worked well, and continued to after I decided to start using OS X. I continued updating all the way up to 10.4.8 (I have avoided updating to 10.4.9 since it caused issues on our IBook). About a year ago the combo drive would come and go (in the system profiler) but the super drive was still working fine. Over the past year strange things began happening. If I would insert a kids games CD it would cause a kernel panic. So I simply used our Ibook to let my daughter play reader rabbit. For about the past 6 months the combo drive has not been recognized in system profiler. But other than the kids cds the super drive seemed to be working well reading & writing both CDs & DVDs. Then it began to error out burning CDs saying they could not be verified but the CDs were turning out ok it was burning DVDs without a problem. Within the last couple weeks it stopped recognizing files correctly. If it is an image or ai document it would say the files could not be opened and it would also not open installers of any kind. I finally decided to try to get it fixed. Last weekend I ran Tech tool & optimized the hard drives and low and behold it was fixed. Combo drive was back & working, Super drive was working correctly & the kids CDs did not cause problems either. This lasted for about 4 days of very infrequent use and all the problems were back. Then yesterday after being off for a couple days I started it up and all was ok again. So I left it on over night planning to make a disk image of it today. At this point I had a theory that my set up might be causing the problem. Since I had been running OS X it was installed and running on a second hard drive I had installed connected to a slave bus while OS 9 was still on the original hard drive connected to the master bus. So I cleaned off the main hard drive and thought since it was working correctly I could transfer the system & apps to the other hard drive and save the working disk image. But of coarse in the middle of transferring files around the combo drive vanished again and the super drive won’t read files correctly. So I decided to reinstall from my OS 10.4 DVD on the main hard drive and reinstall all my apps. But I can’t get it to read or boot up from the DVD. I tried running Tech Tool again with no luck.
Could this be as simple as a bad preference or something?
Here are the machine specs
Machine Name: Power Mac G4
Machine Model: PowerMac3,6
CPU Type: PowerPC G4 (2.1)
Number Of CPUs: 2
CPU Speed: 867 MHz
L2 Cache (per CPU): 256 KB
L3 Cache (per CPU): 1 MB
Memory: 1.75 GB
Bus Speed: 133 MHz
Boot ROM Version: 4.4.8f2
PowerPC G4 dual 867 Mac OS X (10.4.8)

The only thing that seems strange about it being the drives is that whenever the combo drive disappears from the menu the super drive will simultaneously not read files correctly and cause kernel panics etc. And when the combo drive can be seen both drives work with no problems. Would that system still point to failing hardware? It just seems that since it's either both or neither that something that effects them both would be the culprit. Since I posted I was able to reload tiger & after the restart the problem returned. Then another restart it was fine all day. To your point replacement drives are reasonably priced & easy to install so I probably should just get one & try it.
Thanks for your advise
Carl

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