Disk I/O performance (SSD and HDD) very slow

My 2012 MBP (13", 2.5Ghz i5, 8G RAM) has been sluggish for a few months (beachballs now and then, slow to open apps, slow on reboot, etc), going on since perhaps the Yosemite upgrade, but it was never too bad so I didn't worry about it. But it has been annoying so recently I started poking around and found that the disk I/O performance was pretty horrible on both the Corsair 128G SSD (root drive) and the original 500G HDD (secondary). Here's a sample XBench report from my SSD (the numbers from the HDD are similar):

Sequential

Uncached Write: 30.02 MB/s (4k blocks)

Uncached Write: 49.5 MB/s (256k blocks)

Uncached Read: 25.90 MB/s (4k blocks)

Uncached Read: 129.19 MB/s (256k blocks)

Random

Uncached Write: 7.20 MB/s (4k blocks)

Uncached Write: 36.78 MB/s (256k blocks)

Uncached Read: 13.26 MB/s (4k blocks)

Uncached Read: 112.85 MB/s (256k blocks)

This performance has been also measured by Blackmagic and dd's from the command line. I've run through the litany of things to do for good disk health- Repair disk, Fix Permission, turned off FileVault, reset NVRAM/SMC, reinstalled Yosemite. SafeBoot, fsck, you name it...all with no results. There are no disk I/O errors in the console from either disk. All tests were done will all other apps closed and the machine idle. I ran the script Linc Davis has posted in a few other posts and the output is below.

Any ideas about what I should do next to try to figure out what's going on? Any help would be greatly appreciated!

Start time: 23:57:38 06/13/15

Model Identifier: MacBookPro9,2

System Version: OS X 10.10.3 (14D136)

Kernel Version: Darwin 14.3.0

Time since boot: 4 minutes

Memory

BANK 0/DIMM0:

Size: 4 GB

Speed: 1333 MHz

Status: OK

Manufacturer: 0x859B

BANK 1/DIMM0:

Size: 4 GB

Speed: 1333 MHz

Status: OK

Manufacturer: 0x859B

SATA

CORSAIR CMFSSD-128GBG2D

FileVault: Decryption in progress: Percent completed = 6923

Log

Jun 13 23:53:43 com.apple.xpc.launchd.domain.pid.SecurityAgent.303: Path not allowed in target domain: type = uid, path = /System/Library/Frameworks/Security.framework/Versions/A/XPCServices/XPCKeychai nSandboxCheck.xpc/Contents/MacOS/XPCKeychainSandboxCheck error = 1: Operation not permitted, origin = /System/Library/Frameworks/Security.framework/Versions/A/XPCServices/SecurityAg ent.xpc

Jun 13 23:53:43 com.apple.xpc.launchd.domain.pid.SecurityAgent.303: Path not allowed in target domain: type = uid, path = /System/Library/Frameworks/IOKit.framework/Versions/A/XPCServices/IOServiceAuth orizeAgent.xpc/Contents/MacOS/IOServiceAuthorizeAgent error = 1: Operation not permitted, origin = /System/Library/Frameworks/Security.framework/Versions/A/XPCServices/SecurityAg ent.xpc

Jun 13 23:53:43 com.apple.xpc.launchd.domain.pid.SecurityAgent.303: Path not allowed in target domain: type = uid, path = /System/Library/PrivateFrameworks/SpeechRecognitionCore.framework/Versions/A/XP CServices/com.apple.SpeechRecognitionCore.brokerd.xpc/Contents/MacOS/com.apple.S peechRecognitionCore.brokerd error = 1: Operation not permitted, origin = /System/Library/Frameworks/Security.framework/Versions/A/XPCServices/SecurityAg ent.xpc

Jun 13 23:53:43 com.apple.xpc.launchd.domain.pid.SecurityAgent.303: Failed to bootstrap path: path = /System/Library/Frameworks/Security.framework/Versions/A/XPCServices/XPCTimeSta mpingService.xpc, error = 1: Operation not permitted

Jun 13 23:53:43 com.apple.xpc.launchd.domain.pid.SecurityAgent.303: Failed to bootstrap path: path = /System/Library/PrivateFrameworks/DataDetectorsCore.framework/Versions/A/XPCSer vices/DataDetectorsDynamicData.xpc, error = 1: Operation not permitted

Jun 13 23:53:43 com.apple.xpc.launchd.domain.pid.SecurityAgent.303: Failed to bootstrap path: path = /System/Library/PrivateFrameworks/SpeechRecognitionCore.framework/Versions/A/XP CServices/com.apple.SpeechRecognitionCore.brokerd.xpc, error = 1: Operation not permitted

Jun 13 23:53:43 com.apple.xpc.launchd.domain.pid.SecurityAgent.303: Failed to bootstrap path: path = /System/Library/Frameworks/AppKit.framework/Versions/C/XPCServices/SandboxedSer viceRunner.xpc, error = 1: Operation not permitted

Jun 13 23:53:43 com.apple.xpc.launchd.domain.pid.SecurityAgent.303: Failed to bootstrap path: path = /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/Diction aryServices.framework/Versions/A/XPCServices/com.apple.DictionaryServiceHelper.x pc, error = 1: Operation not permitted

Jun 13 23:53:43 com.apple.xpc.launchd.domain.pid.SecurityAgent.303: Failed to bootstrap path: path = /System/Library/Frameworks/IOKit.framework/Versions/A/XPCServices/IOServiceAuth orizeAgent.xpc, error = 1: Operation not permitted

Jun 13 23:53:43 com.apple.xpc.launchd.domain.pid.SecurityAgent.303: Failed to bootstrap path: path = /System/Library/Frameworks/Security.framework/Versions/A/XPCServices/XPCKeychai nSandboxCheck.xpc, error = 1: Operation not permitted

Jun 13 23:53:43 com.apple.xpc.launchd.domain.pid.SecurityAgent.303: Path not allowed in target domain: type = uid, path = /System/Library/Frameworks/AppKit.framework/Versions/C/XPCServices/SandboxedSer viceRunner.xpc/Contents/MacOS/SandboxedServiceRunner error = 1: Operation not permitted, origin = /System/Library/Frameworks/Security.framework/Versions/A/XPCServices/SecurityAg ent.xpc

Jun 13 23:53:43 com.apple.xpc.launchd.domain.pid.SecurityAgent.303: Path not allowed in target domain: type = uid, path = /System/Library/PrivateFrameworks/SpeechRecognitionCore.framework/Versions/A/XP CServices/com.apple.SpeechRecognitionCore.brokerd.xpc/Contents/MacOS/com.apple.S peechRecognitionCore.brokerd error = 1: Operation not permitted, origin = /System/Library/Frameworks/Security.framework/Versions/A/XPCServices/SecurityAg ent.xpc

Jun 13 23:53:43 com.apple.xpc.launchd.domain.pid.SecurityAgent.303: Path not allowed in target domain: type = uid, path = /System/Library/PrivateFrameworks/DataDetectorsCore.framework/Versions/A/XPCSer vices/DataDetectorsDynamicData.xpc/Contents/MacOS/DataDetectorsDynamicData error = 1: Operation not permitted, origin = /System/Library/Frameworks/Security.framework/Versions/A/XPCServices/SecurityAg ent.xpc

Jun 13 23:53:43 com.apple.xpc.launchd.domain.pid.SecurityAgent.303: Path not allowed in target domain: type = uid, path = /System/Library/PrivateFrameworks/GeoServices.framework/Versions/A/XPCServices/ com.apple.geod.xpc/Contents/MacOS/com.apple.geod error = 1: Operation not permitted, origin = /System/Library/Frameworks/Security.framework/Versions/A/XPCServices/SecurityAg ent.xpc

Jun 13 23:54:02 com.amazon.cloud-player: Service setup event to handle failure and will not launch until it fires.

Jun 13 23:54:02 net.tunnelblick.tunnelblick.LaunchAtLogin: Service setup event to handle failure and will not launch until it fires.

Jun 13 23:54:13 com.apple.spindump: Service exited with abnormal code: 75

Jun 13 23:54:23 com.apple.spindump: Service exited with abnormal code: 75

Jun 13 23:54:33 com.apple.spindump: Service exited with abnormal code: 75

Jun 13 23:54:43 com.apple.spindump: Service exited with abnormal code: 75

Jun 13 23:54:53 com.apple.spindump: Service exited with abnormal code: 75

Jun 13 23:55:03 com.apple.spindump: Service exited with abnormal code: 75

Jun 13 23:55:13 com.apple.spindump: Service exited with abnormal code: 75

Jun 13 23:55:23 com.apple.spindump: Service exited with abnormal code: 75

Jun 13 23:55:33 com.apple.spindump: Service exited with abnormal code: 75

Activity

I/O: 346 ops/s, 130773 blocks/s

Descriptors: Google\x20Chrome\x20H (UID 501) is using 8422 files

kexts

org.virtualbox.kext.VBoxDrv (4.3.28)

org.virtualbox.kext.VBoxUSB (4.3.28)

org.virtualbox.kext.VBoxNetFlt (4.3.28)

org.virtualbox.kext.VBoxNetAdp (4.3.28)

Daemons

org.postfix.master

com.barebones.authd

com.oracle.java.JavaUpdateHelper

com.backblaze.bzserv

org.cups.cupsd

com.oracle.java.Helper-Tool

com.vix.cron

org.ntp.ntpd

org.macosforge.xquartz.privileged_startx

Agents

org.openbsd.ssh-agent

com.backblaze.bzbmenu

com.adobe.ARM.UUID

com.valvesoftware.steamclean

org.macosforge.xquartz.startx

com.oracle.java.Java-Updater

com.spotify.webhelper

net.tunnelblick.tunnelblick.LaunchAtLogin

com.amazon.music

com.amazon.cloud-player

com.google.keystone.user.agent

App extensions

com.getdropbox.dropbox.garcon

Apps

/Applications/Dropbox.app

DNS: 8.8.8.8 (static)

Listeners

kdc: kerberos

launchd: afpovertcp

User login items

Flux

- /Applications/Flux.app

Jumpcut

- /Applications/Jumpcut.app

BetterTouchTool

- /Applications/BetterTouchTool.app

Restricted files: 251

Elapsed time (s): 69