seeing as I've taken countless L61s apart, and tore down an LSJ to practically nothing, and I have an LS61 (L61 head+ LSJ block) in my car at the moment, allow me to elaborate (much like airtonics did)
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1.) take an LSJ engine (oil pan, block, head, header, intake monifold, s/c) from the junkyard,
thats fine. They can usually be had for $2500 out of a junkyard for a complete engine (including s/c and harness)
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2.) installed the L61 valve cover (since the the bolts for the middle cover, or CDI in the L61, are different), so one can put on the L61 CDI,
Can't put the L61 valve cover on the LSJ, the LSJ has two flanges on the backside of the engine (driver side if you think sideways FWD style) and the L61 valve cover only has one bump (where the power steering mounts).
L61 head:
LSJ head:
you can only use the appropriate valve cover (cam cover, whatever you wanna call it) with the matching head.
The ignition systems will also only bolt onto their matching valve cover. I'll double check this tonight since I have both an L61 ignition and LSJ ignition sitting at home.
The LSJ also uses different style spark plugs than the L61. I'm pretty sure the cobalts have a small washer to seal, while the L61 has a taper seat.
Another risk is that the flange for the cam sensor on the LSJ (the one closest to the firewall, or to the left in the picture above) has a possibility of running into the brake booster of the Jbody. Since nobody has tried that yet, its still not really known whether or not it would physically fit.
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3.) connect the L61 harness to the sensors on the LSJ block,
several problems here.
first, the LSJ moves some sensors around. The coolant temperature sensor being the biggie. The L61 has its sensor on the back by the thermostat housing. The LSJ has it in the head near the upper coolant hose. You'd have to cut and extend the wire to way up there, but this also leads to another problem...
the LSJ has an oil cooler, which gets in the way of the L61 thermostat housing. The LSJ's thermostat housing interferes A LOT with the F23 transmission.
You can either make a bypass hose for the cooler by threading into the sleeves in the oil filter boss, or some other way. YOU CANNOT just block them off, because the cooler is situated so that oil is forced to go through it. Blocking both holes off will cut off oil recirculation, and starve the engine of oil. If you bypass the cooler, you can use the L61 thermostat housing no problem, as well as the L61 lower radiator hose.
The problem with this is I'd want to keep the cooler since you want the supercharger, AND the LSJ has piston squirters and while I'm no genius engineer, I'd imagine they absorb quite a bit of heat from the underside of the pistons (why they're there) so the cooler probably helps keep the oil from getting heated, and keeps the engine and oil healthy.
If you do keep the cooler, you have to re-arrange your coolant hoses because you now have 2 extra connections for the oil cooler (its plumbed with coolant to cool the oil.. yes an oil to water cooler)
secondly, no one (including myself) knows quite how the LSJ will interact with the F23 transmission yet. The LSJ has an 8 bolt flywheel and a larger diameter clutch. The O.D. is the same so it fits inside the bellhousing no problem, but the depth of the clutch is different, and the bolt patterns are VERY different from L61 clutches so its impossible to make a hybrid of the two, you have to use either one or the other (I'm using a stock cobalt SS clutch with my F23 transmission, and a cavalier clutch actuator.. still HOPING it works but I haven't finished the project just yet)
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4.) maintain the (in my case) automatic transmission from the L61 and bolt it on to the LSJ (I'm not sure on the bolt pattern, though, but I am pretty sure they would be the same since it is the same basic block),
The bolt pattern is indeed the same, but getting a flex plate and a torque converter for the LSJ might be hard since they were never offered with an automatic transmission. Custom units could be ordered I suppose. IDK if the thermostat housing will interfere with the auto or not.
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5.) install an aftermarket fuel pump (or maybe even the LSJ fuel pump),
I would leave the LSJ fuel pump alone. Racetronix is the best in-tank fuel pump upgrade for the jbody at the time (unless you go insane)
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6.) take the resovoir, aftercooler and pump from the LSJ and adapted it to the Cavalier like bolting on an intercooler,
ok
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7.) if the lower mount and/or oil pan is different then excahnge the LSJ with L61 oil pan and lower bracket,
L61 pan has to go onto the LSJ block.
You also need to use the L61 upper engine mount, the cast aluminum peice that bolts to the block just above the timing chain access cover (the LSJ's cast engine mount is different) as well as the L61 alternator, and belt tensioner.
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8.) and take the Cavalier to a GM dealer and have them reprogram the PCM for the GM Cavlaier/Sunfire Supercharger Kit #17800003 (although that reprogram is for 8 psi or boost not the LSJ 12 psi, maybe slip the tech a 20 to boost up the fuel table).
this is your major oversight. The L61 has a 6+1 reluctor ring that is CAST onto the crankshaft. This tells the crankshaft position sensor where it is, and gives it a reference for the ignition system (as well as the fuel injection system)
the LSJ on the other hand, has a 60-2 reluctor ring thats bolted on. Getting to it however, requires disassembly of the block and removal of the crankshaft.
you can use a trigger wheel and feed the sensor signal to the jbody pcm and get the reflash.
or, you could have a custom trigger wheel made and bolt it into the LSJ (again you have to COMPLETELY DISASSEMBLE the bottom end to get to it.
or, you can run a megasquirt or other stand alone computer system. the jbody ecu is not something you really want to retain.. like, ever.
quick breakdown:
L61 (2.2 n/a)
86mm bore 94.6mm stroke
cast crank, 1015 steel rods, cast pistons (dish)
10:1 compression ratio
lost foam cast head
one cam flange
7 tooth trigger wheel (6+1)
6 bolt flywheel
5 rib serpentine belt
wasted spark coils on plug (twin coils)
"compression sense" cam source generator
LSJ (2.0 s/c)
86mm bore 86mm stroke
forged steel crank, 5115 steel rods, cast Mahle pistons (donut dish)
9.5:1 compression
sand cast head
two cam flanges
58 tooth trigger wheel (60-2)
8 bolt flywheel
6 rib serpentine belt (reverse spun alternator)
true coil on plug ignition (four coils)
cam sensor spun by exhaust cam
note: you CANNOT mix and match rotating assembly components (crank, rods, pistons) they have to be a matching set. However, it is possible to use a L61 rotating assembly in an LSJ block, or an LSJ assembly in an L61 block.
with all that said, here's my advice:
an LSJ/L61 hybrid isn't for the faint of heart (or someone with money or wife problems). If anything, buy a fresh L61 out of the junkyard (much lower mileage) and bolt the s/c kit onto it and be done. The amount of work you're looking at doing is NOT for someone who isn't prepared to throw a lot of cash at their car.