That particular assembly step could use a little more Design For Manufacturing work, especially where it's the end-user who is doing the final assembly.  I used heat-sink compound to hopefully get a better thermal connection to the block.

Assembling the E3D was overall really straightforward. I followed Thomas Sanladerer's guide along with the E3D assembly wiki (sorry, can't post links yet). The only issue I had was dealing with the thermistor. Assembling the fiberglass insulation and crimp leads was no problem, but I'm a little unsure about how well I was able to install it on the heater block. The hole really didn't have enough room for the insulation to fit in smoothly and the bulb didn't go into the block very far (I wasn't able to hit the 5mm depth), so I'm not 100% convinced I was able to put it together properly. Figure 1 shows their image (left) and my attempt (right). The fiberglass wound up getting frayed around the hole so I'm not too inclined to keep taking it apart. I don't have my multimeter on hand so I won't be able to check if it's properly insulated until Monday. I feel like they may have tweaked the design to have a smaller diameter hole with a smaller depth because the product I got didn't really match up with what I was seeing in the tutorials. On the other hand, this could entirely be my bad!

Let's move on to the Mk5 mount. I bought these pieces off of Filastruder (for obvious reasons!) and they fit very nicely together onto the carriage (Figure 2). The left screw hole on the filament guide is too shallow for any of the original screws to fully tighten onto, but the right side works just fine and will hold everything in place. The tension arm only had enough clearance on the axle/screw for the roller and three out of the four spacers so for the time being the roller is a little off-center. In the future I might go back to the original tension arm but I had to use some of the screws from that assembly for the new mount so that is out for now. I don't see it being a problem though. Now, there is one major shortcoming of this design. The mount ("v6 E3D MK5 Body for Solidoodle" on thingiverse) holds onto the E3D with a snap fit which doesn't do a very good job of keeping it steady. There is a lot of front/back wobble (Figure 3) on the cold end that will mess with prints. Because of this I'm probably going to zip-tie some old junk parts onto the front to try to hold the hotend in place while I print a better mount. If anyone knows of a design with an arm that screws over the front that would help tremendously.

I was going to try to attach the thermistor and heater to the existing wire connectors but that's going to be a huge pain. For now I'm just going to run the wires all the way back to the board and splice the fan into the extruder motor wiring. I might revisit this part somewhere down the line but at this point I just want to start printing again.

My board is an ATMEGA644P on a Sanguinololu. Once I get everything wired up I'm going to follow the Firmware instructions on the Soliwiki E3D extruder page then go from there. Let me know if there's anything new I should look out for, I'll post updates once I have 'em!

https://github.com/ozadr1an/Solidoodle- … in_v1_beta

Do you need instructions as well? I will need to know what board is on your printer, guessing it is a Sang?

Save yourself the heart ache and order an E3d from Filastruder, they also sell the MK-5 mount to replace the acrylic. 
I only say this because even if you manage to clear that clog it will happen again with in the next couple of prints.  I have owned several SD3's and switching to the E3d is the first thing I do.  I have tried to clear clogs on the stock hotend and it just seems to get worse and worse.  With the E3d I never have clogs and I would never switch back to the PEEK style hotends.
I know this isn't what you were hoping to hear but it will save you money and time in the long run.

Thanks for the info, I spent some more time poking around online and pretty much came back to this. Sort of a bummer to put down the money but it's not really all that expensive considering it's the business end of the entire machine. Can't help but find it funny that I could have printed my own mk5 mount and feed system if only the printer still worked, but what are you gonna do?

I ordered an E3d v6 with a compatible mk5 extruder assembly, should be in around Thursday. I looked up some guides for setting up the E3d and one place talked about needing a beefier power supply, any word on how necessary that is? My SD3 never struggled to run everything on the stock power supply and the ones they recommend seem like serious overkill.

Save yourself the heart ache and order an E3d from Filastruder, they also sell the MK-5 mount to replace the acrylic. 
I only say this because even if you manage to clear that clog it will happen again with in the next couple of prints.  I have owned several SD3's and switching to the E3d is the first thing I do.  I have tried to clear clogs on the stock hotend and it just seems to get worse and worse.  With the E3d I never have clogs and I would never switch back to the PEEK style hotends.
I know this isn't what you were hoping to hear but it will save you money and time in the long run.

+100
Your current hot end is DOA I'm afraid...

I had set up a long-ish print and left it unsupervised. When I came back it looked like the printer had randomly stopped extruding for two or three layers, then picked back up and carried on the print. This left some bands of missing perimeter on the print but it wasn't catastrophic enough to wreck the print so I didn't think too much of it. Unfortunately I tossed the parts without taking any pictures so I can't show you what I'm talking about.

It happened again on another large print, but this time it didn't clear up. I'm not sure how long it was running for before I caught it but it had about half an inch of clearance between the top of the part and the nozzle, so I'd say it probably went for ~40 layers in this state. I killed the print and figured the nozzle was clogged so I tried to retract the filament so I could clear the nozzle with some wire, but the filament wouldn't retract (I had the extruder at ~190C). In fact, I couldn't even pull the filament out of the top with my hands. At this point I had to drop this for about a month because I was too busy to do a tear-down.

Fast-forward to today. I tried once again to extrude or retract with the nozzle at 200C, but still nothing. The filament was still totally jammed up somewhere in the extruder. I found the unclogging procedures page (Can't post the link) and figured this had to be a cold jam. I tried to pull the PLA filament out of the top again until it sheared off about 1/4" above the acrylic section (Image_1 & 2). I tried to push the remaining plastic through with a hex wrench (as in the unclogging procedures page) but it wouldn't budge. Finally, I took apart the entire assembly and got a look at the actual jam. It looks pretty bad, I got some close-ups in the picture dump but it looks like the PEEK insulator and PLA got really badly deformed and completely seized up (Image_3 & 4).

I'm not sure where to go from here, if anyone can help out I'd really appreciate it. I might have to replace some things but I'm hoping to avoid that somehow.