I'm not aware of any issues like yours with the Intel(R) Matrix Storage Manager 8.8. It seems to me like you have a power issue.
Try connecting your hard drives to different ports on your power supply and look for a power supply calculator online and see if your system is underpowered.
Also, check on the basics, SATA cables, power cables and grounding. Download a test utility from the hard drive manufacturer web site, it can give you an idea if your hard drives are having problems.
And you should not get any problems installing the Intel® Rapid Storage Technology 9.5 once you have the Intel(R) Matrix Storage Manager 8.8.
The question of RAID systems indicating that drives have failed, when they are in fact OK, comes up time and again in RAID discussions.
The answer to you problem is probably quite simple.
A standard drive has an error recovery routine built into its firmware that is NOT compatible with most RAID setups, and the drives that you have installed in your RAID unfortuately are such standard drives.
Western Digital manufacture RAID-specific hard drives that have inbuilt a firmware routine called "Time Limited Error Recovery".
A standard drive may take several minutes to complete its error recovery routine, whereas RAID controllers will only allow about 7 seconds to complete a drive error recovery - thus a conflict. If a hard drive takes longer than that 7 seconds to complete an error recovery, which a standard hard drive will typically do, then the RAID controller will mark that hard drive as failed - when, in fact, it has not.
The solution is to install hard drives which have each hard drive manufacturer's form of "Time Limited Error Recovery".
For further information I suggest you look up "error recovery" on each manufacturer's web site, and you will find articles explaining this problem and referring you to that manufacturer's RAID-specific hard drives, and their particular form of Western Digital's "Time Limited Error Recovery".
I hope that I have properly understood your problem, and that this contribution helps.