SMB writing Speeds (Mavericks 10.9.5, Server 3.2.2)

Hello all,
In our network we have a vast majority of Mac based machines, primarily Mt. Lion, but a good handful of Mavericks clients and a few Yosemite clients now as well. We also have a few Windows based machines that freelancers use.
Our server is a 2012 Mac Mini with 2 SSDs and it's connected to the network over a 1 Gb connection. It's running 10.9.5 with server 3.2.2. Also, our server has been optimized following the instructions at http://rolande.wordpress.com/2014/05/17/performance-tuning-the-network-stack-on- mac-os-x-part-2/
We've always used AFP as our file sharing protocol for our Macs and SMB for the PCs, however, with the Mavericks clients (all running 10.9.5) it's my understanding that unless a user uses the "Connect To Server" dialog and connects via the AFP protocol, Mavericks will default to SMB2. Our Mavericks clients have always reported issues when they use the Bonjour listing to connect to the server (because I believe it's defaulting to SMB) so we've forced them to connect via AFP using the "Connect to Server" option in find.. I've also seen numerous posts about how unreliable SMB was when Mavericks first launched.
I finally had some time, so I decided to do a speed test comparison between AFP, SMB, and CIFS (what most of the SMB posts recommend using to connect to SMB shares) protocols. To do this, I used a perl script that I obtained from http://hintsforums.macworld.com/showthread.php?t=168289 with a 243MB file. The client I used was my Yosemite test machine, running 10.10 final release, as I wanted to see if the SMB protocol updates in Yosemite cleared things up. In my tests I both wrote to the server and saved a local copy of the file to my desktop from the server using all three protocols. My data is below, but suffice it to say, it shows a drastic speed differential when writing to the Mavericks Server.
When writing to the server, AFP had an average write rate of 10620.8 KB/s (transfer time of 22.66 sec), SMB had an average of 2430.9 KB/s (transfer time of 98.05 sec), and CIFS had an average of 2422.0 KB/s (transfer time of 98.40 sec). The difference between SMB and CIFS was negligible (as one would expect), but the AFP speed was almost 4.5x faster.
When writing the file from the server to my desktop, AFP had an average write rate of 948575.9 KB/s (transfer time of 22.38 sec), SMB had an average of 815190.8 KB/s (transfer time of 23.92 sec), and CIFS had an average of 574321.2 KB/s (transfer time of 29.19 sec). Again the AFP was faster, but barely so, but both SMB and CIFS speeds drastically increased.
My question is, has any one been able to optimize settings on the Server to increase the speed at which it can receive SMB files? Ideally I would love to figure out a way to get transfer speeds to the server over SMB closer to those of AFP or even the transfer from speeds over SMB. If this is possible, I would consider dropping the AFP protocol entirely and moving systems over to SMB, as many of our systems will be upgraded to Yosemite in the coming months.
Thanks for your thoughts!
Data from tests:
AFP:
WRITING TO SERVER
22.66 s: 243138560 bytes (read:1877171.0 KB/s write:2218474.8 KB/s copy:1016801.0 KB/s)
22.66 s: 243141593 bytes (read:185420.4 KB/s write:2484633.6 KB/s copy:172544.0 KB/s)
23.40 s: files are closed
Peak read rate:  2375535.0 KB/s
Peak write rate: 2484633.6 KB/s
Peak copy rate:  1162058.3 KB/s
Average read rate:     773099.2 KB/s
Average write rate:     10620.8 KB/s
Average transfer rate:  10147.4 KB/s
WRITING TO DESKTOP FROM SERVER
22.38 s: 243138560 bytes (read:1636801.6 KB/s write:1362616.5 KB/s copy:743588.5 KB/s)
22.38 s: 243141593 bytes (read:157255.3 KB/s copy:157255.3 KB/s)
22.40 s: files are closed
Peak read rate:  1945184.5 KB/s
Peak write rate: 1483068.8 KB/s
Peak copy rate:  820903.5 KB/s
Average read rate:      10729.5 KB/s
Average write rate:    948575.9 KB/s
Average transfer rate:  10599.7 KB/s
smb:
WRITING TO SERVER
98.05 s: 243138560 bytes (read:831069.5 KB/s write:2260.7 KB/s copy:2254.5 KB/s)
98.05 s: 243141593 bytes (read:37532.2 KB/s write:3105792.0 KB/s copy:37084.1 KB/s)
98.11 s: files are closed
Peak read rate:  1231355.3 KB/s
Peak write rate: 3105792.0 KB/s
Peak copy rate:   37084.1 KB/s
Average read rate:     637277.9 KB/s
Average write rate:      2430.9 KB/s
Average transfer rate:   2420.3 KB/s
WRITING TO DESKTOP FROM SERVER
23.88 s: 243138560 bytes (read:1945184.5 KB/s write:1335499.8 KB/s copy:791845.0 KB/s)
23.88 s: 243141593 bytes (read:163462.7 KB/s copy:163462.7 KB/s)
23.92 s: files are closed
Peak read rate:  2130440.1 KB/s
Peak write rate: 1491308.1 KB/s
Peak copy rate:  854890.0 KB/s
Average read rate:      10065.8 KB/s
Average write rate:    815190.8 KB/s
Average transfer rate:   9926.8 KB/s
CIFS:
WRITING TO SERVER
98.40 s: 243138560 bytes (read:639132.0 KB/s write:2710.9 KB/s copy:2699.5 KB/s)
98.40 s: 243141593 bytes (read:49298.3 KB/s write:3105792.0 KB/s copy:48528.0 KB/s)
98.46 s: files are closed
Peak read rate:  1203746.4 KB/s
Peak write rate: 3105792.0 KB/s
Peak copy rate:   48528.0 KB/s
Average read rate:     648413.5 KB/s
Average write rate:      2422.0 KB/s
Average transfer rate:   2411.5 KB/s
WRITING TO DESKTOP FROM SERVER
29.14 s: 243138560 bytes (read:1931190.3 KB/s write:1362616.5 KB/s copy:798915.0 KB/s)
29.14 s: 243141593 bytes (read:165642.2 KB/s copy:165642.2 KB/s)
29.19 s: files are closed
Peak read rate:  2130440.1 KB/s
Peak write rate: 1491308.1 KB/s
Peak copy rate:  854890.0 KB/s
Average read rate:       8266.5 KB/s
Average write rate:    574321.2 KB/s
Average transfer rate:   8135.3 KB/s

Hi Linc,
Thanks for the reply.
The Time Machine folders shown are from the Server app Storage tab which shows all connected hard drives. I haven't set TM drives up to be shared and hopefully the following screenshots will illustrate the current setup. This setup was created from a clean install of all involved software i.e. drives were erased and setup from scratch and the TM drives were simply connected and TM took control from there.
As you can see from these screenshots, when viewing the permissions through the Server app, there appears to be an extra user when compared to the OS Get Info window.
After leaving TM to its own devices over the weekend, I was greeted with a 'preparing backup' message this morning(Mon 13th October), with a last backup completed on Sat 11th October at 15:19:16. Stopping this backup and starting a manual backup has now resulted in a new, never before experienced error message stating that the backup disks can not be found:
Console reports:
I must re-iterate, the disk was erased and simply connected and Time Machine did its thing. Now as 'admin' it is clear that the folders created by TM do not have permissions so that I can simply view them in Finder, but does this directly affect TMs ability to access folders it has created itself?
One useful bit of information I seem to have neglected is that the erased TM drive is encrypted, however the password was entered when the drive was connected to the machine and there has been no prompt thereafter.
Please help. Only other comment I can make is that before the update to Mavericks and Server app 3.2.1, none of this was a problem.

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