I am mostly wondering about the possibility of: offset grinding the connecting rod journals to gain a little more leverage and travel. Lets say a .025 increase.

New custom pistons can't be much MORE expensive than factory sized standard replacements. (or maybe they can be...)

And over boring the liners.. I have not found much information on factory oversized pistons as of yet but if one was to increase the stroke, then why not overbore as well?

What are your thoughts on this?

As to "why" I am mostly just wondering.. but I do have a running engine sitting in the barn, and would like to install it in my mid 60's Dodge truck, so the more low end torque, the better.

nope,
and a very few have talked about an aftermarket cam, which i doubt you could find a cam maker who would consider it

Why bore and stroke the engine to increase displacement, when what you need most on our engines is more fuel. Likewise, I've not heard of any cams, cranks, or way oversized pistons for our engine, so I'd be inclined to believe they don't have any on the market, but I may be wrong.

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1984 300sd auto with 246,000 miles

For the cost of a Myna modified pump and a bigger turbo, intercooler , better exhaust, you could actually gain enough power to justify putting it in a pickup and having decent power. The small increase in displacement you would get from boring and stroking would not help much. The stock IP is just about maxed out in any case, if you dont add more fuel you wont get any more power no matter what displacement you end up with. The nice part is that the stock engine parts will withstand a modest increase in power without breaking. Cheers

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It's always something simple
91 300D 603.960 (from japan) 194K
92 Toyota Diesel Landcruiser HDJ81-t 116K
02 Golf TDI new head courtesy of PO
87 300D
97 BMW 525 TDS Wagon 5spd
bunch of Onan and other diesel generators

If you're going to rebuild, I've heard that gapless rings, stronger rods, ARP studs, and a custom MLS heatgasket are the way to go.

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$60 OM617 Blank Exhaust Flanges
$110 OM606 Blank Exhaust Flanges
No merc at the moment

I agree with Bigblockchevy and others about boring and stroking this engine. You won't get the power that way. Do the math, your displacement will barely increase.
Helpful Engine Calculators - Wiseco Piston Inc.
Check out youtube for what people have achieved by modifying the pump and the turbo.
Btw, it's not cheap!
European Highly tuned Mercedes Benz Diesel Racing, Drag Strip - Smokey! - YouTube
Which ever way you go with it good luck.

Three liters out of only five pots is plenty big enough. The funky valve train, non-crossflow head design and oddball MW injection pumps keep me from considering hopping up these tractor engines. Your money is better spent investing in the much more modern OM60X designs if you want to build up a go-fast unit.