You can go either way - pull the engine only, or pull engine and trans. However, I find that it's usually easier to pull engine/trans together on front-wheel drive (back when I actually used to work on that crap) than it is to pull both together with RWD or 4WD - and the 242 tips at a little short of 500#! That big, I'd like to keep it small, so I can handle it easier.
Given a choice, I'll pull the engine with the manifolds in place - the same way I pull the head. I might actually pull the head first, then pull the short block (you'd then have the head bolt holes and more options to attach the puller.) You can then use SAE Grade 8 bolts in 1/2-13 to attach the chain, and leave yourself a little room so you don't whack the chain links into the deck. I'd also suggest hardened washers under the bolt heads (to hold the chain) and "cleaned" fender washers between the chain and the block deck (so the chain doesn't booger it up - the chain is harder than the cast iron engine. By "cleaned," I mean take a few minutes to find and remove any sharp edges or stamping flash, and round off all the inside and outside radii. Use brass, if you can find it.)
Stroking the 242 can be as easy - or as hard - as you can make it. It's theoretically possible to stroke the engine "in place" - without pulling the block - but with the issues you're talking about, you're probably better off pulling the block. Have it boiled and checked out by a decent machine shop, and see if they recommend boring the cylinders to clean them up. Accept the minimum bore you can (usually .030" over,) unless you have a reason to go larger. You'll need to know the final bore size before you can buy pistons and rings.
Meanwhile, you can go ahead and get your crankshaft and rods - you'll need the crankshaft and connecting rods from a 258 engine. There are, as I recall, three different 258 cranks out there - they all have their own peculiar advantages - and the difference is in the number of counterweights they use.
Four-weight - a good crankshaft for running at high speeds and when rapid throttle response is desired. The overall lighter crankshaft - coupled with the lower "moment arm" from fewer weights - will also help to cut parasitic drag. You should only really look for one of these if you plan on getting silly.
Eight-weight (or is it six? I'd have to check..) - The middle ground. Eight counterweights offer more precise balancing with a good machinist (or at least one that gives a damn,) but the crankshaft is heavier, which means it takes more torque to spin it and throttle response will be slower than the four-weight - but you're not building a ricer, so that's not much of an issue.
Twelve-weight - This is the big one, and it's usually harder to find. Works well with manual transmissions, since the extra counterweights work kinda like an "inertia ring" that would be put in the flywheel. The extra intertia will help to reduce stalling at takeoffs, but it will also (slightly) delay throttle response - again, not a huge issue, since we're not building little four-popper riceboy engines here.
The inline six is usually considered as a powerplant designed to make good useful low-end torque, and to spin at a given speed all day long - that's what it does well. That's why Cummins still specialises in the inline six Diesel, and why they're damn good engines.
The crankshaft weight is not as great a problem as it could be, since I6's aren't designed to spin up around 10,000-12,000 RPM like V8's and those puny little I4's. A redline of 6,000 RPM is plenty for us.
If you are able to follow instructions, you should be able to assemble the stroker yourself once you have the block seen to and the parts in hand - only a few special tools are needed - and they're commonly available. As far as paying for it, if you provide the parts, the going rate for assembling an engine (check your machinist's bill of services,) should apply - no special work is necessary beyond any boring of the block. Crank/rod clearance isn't really an issue until you get up around a 4" stroke. If you are confident in your ability to assemble an engine properly, it should be no trouble for you to do the "stroker" mod.
When pulling the engine, you'll pick up some space if you pull the fan and fan clutch off the front - or just pull the AC compressor aside and remove that bracket. (Granted, this is advice for RENIX only!) There is a hidden bolt at the bottom of that bracket - but getting it out is worth about 3" of extra clearance up front, and that's not a little!
The only advice I can really give is specific to RENIX at the moment (that's all I've got - four RENIX XJ's,) but if you tell us more about what you're working on, you will get better advice. Just trying to help...
5-90
if it's a manual, just pull the clutch out on the flywheel and service it outside the vehicle. Either way, there are only four bolts that hold the engine to the transmission. You'll make it easier on yourself if you lower the transmission to reach the upper bolts, the loosely bolt the crossmember back up while you're pulling the engine.
