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what are the chances that the transmission and transfer case shift levers are going to match up with my existing 3sp tunnel holes? ..... should I remove the access panel prior to installation and prepare to modify it? ......
I really don't know. My 71 was originally 3 on the tree with a vacuum actuated t-case. When it was converted to 3 on the floor, the hole cut into the tunnel for the shifter matched up when I put in the 4 speed transmission. You should plan to remove the transmission hump cover, at a minimum it will improve access for installation.
To all the forum members that have swapped an engine/drivetrain .....
What should I look for and/or replace while I have the complete drivetrain out of the vehicle? .... i.e. what preventive maintenance is best to do now while I have such good access? ....
You should look to achieve a balance (between risk mitigation, time and dollars) that you will be comfortable with. At a minimum you should visually inspect everything. Are there tell tale signs of leaks? Are there cracks? Go ahead and remove the parking brake drum and inspect the shoes.
Beyond the visual inspection, you might consider replacing all gaskets and seals. If you go with replacing gaskets and seals, you will be dropping the oil pan, so you might consider inspecting the bearings and the oil pump gears. If you did any of the previous, you have already seperated the transmission from the bellhousing, so you should inspect the clutch and flywheel. And as long as you have gone this far, you might consider seperating the t-case from the tranny and replacing all the gaskets - of course while you have them opened up you might consider measuring all the clearances.
Presuming the inspections don't find any issues, you have put in a few hours time and few dollars (ok more than a few less than a couple of hundred) in gaskets and seals - and you will have put eyes and gauges to just about everything. Of course, if your inspections find issues you will put in more time and dollars to address the issues. Every issue that you take care of now, is an issue that you likely won't have to revisit for a long, long time.
The balance for each individual and their circumstances is different. In my case, I replaced gaskets and seals, turned the flywheel, bought a new clutch and slapped a used engine, tranny and t-case right into my truck. It ran great and I was happy. A few months later, I had a cracked block and pulled the whole works out, rebuilt an engine and then installed it all back. Knowing what I know now, I would have been time and dollars ahead if I had rebuilt the engine (and learned at that time about the cracked block) when I was at the same stage as where you are at. That said, I would do it all the same way because (for me) it was the right balance and what I was comfortable with at the time.
Getting back to the specifics of your situation. Take some measurements of the flanges on the t-case where the drive shafts attach and then measure the flanges on the differentials. You will likely find the size and spacing of the holes is different. In addition to driveshaft lengths, this is another issue that has to be addressed when putting a 4 speed into the earlier FJ40s. There are many ways to address the issue, but perhaps the most straight forward approach is to call Kurt at Cruiser Outfitters and buy new flanges for the differentials.
