Got the oil pan back on today after finally receiving all the correct con rod bolts from overseas. I'll be stabbing the trans and transfer onto the engine in the next 3 days (hopefully).
I'm currently looking at how I'm going to modify the rear crossmember mount, namely the threaded "nutserts" that exist in the framerail. I've got a pretty good plan which should be very "factory" in appearance when finished. More on that later.
I also pulled out the automatic trans shift assembly today as I'm going to modify the metal base (as Nick did) to accept all the 5 speed shift boots and the 5 speed ABS shift console. This pic shows all the rubber seals, grommets, and electrical relays removed. What you're left with is a bunch of spot welded on mounts which need to go. That, and it's super crusty from the gallons of soda and coffee that were likely spilled on it. The media blaster will take care of that.
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The only two brackets that need to be retained are the rearmost pair. The rear of the ABS 5 speed console will bolt up to them. DON'T CUT THEM OFF but remove everything else.
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All the sad little bits are now removed. I used a BLAIR spot weld cutter, they work excellent and I bought an entire kit when I did a bunch of sheet metal work on my FJ40. All you need is a center punch and a hand drill. They cut around the spot weld removing the piece you want to get rid of but they won't ruin the metal underneath (if you're careful). I also used a DREMEL with a cutting wheel to break the welds on the large shift pin/rod.
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All that's left behind is the little spot weld "nubbin" if you will. I'll grind all these off and smooth everything out with some 3M pads in the future. I'm using the automatic shift plate during this conversion because as Nick pointed out in his thread, you're able to use all the factory "nutserts" which are already in the floorpan and you'll also get a very good air/heat seal around the floor. After the trans goes in, this piece will require some more mods.