I can offer zero support on any other engine suggestions, but I would wholeheartedly swap any new components from the original engine to the replacement engine in a heartbeat.
Engine replacement suggestions
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I agree with Long, it makes sense to take your new water pump and timing components and swap them onto the "new" engine. Obviously that will be more work, but with the timing components being such an important factor in the health of these engines, it would be good to know the condition of what's on the "new" engine before you swap it in.
For the A/C, I think you'll just need to experiment yourself to see if you can leave the compressor hooked up and just move it out of the way. I've done it that way on a couple of different cars and it definitely makes life easier.
I've done a couple of engine replacements with used engines on my '90s Subaru. I never know what to check. On Youtube you can find videos of people that turn their engine stand into a test rig - build a fuel system and wire up the ECU and everything, actually start the engine and run it. At the pace I work, it would take me weeks to do all of that, by which time if I did find something wrong the place I got it from would be like, "Tough patooties, your warranty expired 3 months ago!"
In your case, if you go ahead and replace the timing components and water pump, you're already going to be giving the engine a pretty good once-over, probably more than most folks would do, so I think you'll be ahead of the game.
As for lubing the engine, if you're pulling the valve covers to inspect the cams, anyway, I'd put assembly lube all over them - bearing surfaces, lobes, tips of the valves (if you can reach them), etc. You can lube all the timing components as you're replacing those. Is there a way to pre-lube the V6s? On LS engines there's a port on the front driver side of the block that you can screw a 16mm-1.5 adapter into and hook up a hose to pump oil through the engine before you start it, so that's what I did when I had to replace my LS6. If you can't do something like that, then you can at least crank the engine over with the starter for a while before you actually start it - that'll get the oil pump to do its job and circulate oil through everything while there's no load on the engine.
For the A/C, I think you'll just need to experiment yourself to see if you can leave the compressor hooked up and just move it out of the way. I've done it that way on a couple of different cars and it definitely makes life easier.
I've done a couple of engine replacements with used engines on my '90s Subaru. I never know what to check. On Youtube you can find videos of people that turn their engine stand into a test rig - build a fuel system and wire up the ECU and everything, actually start the engine and run it. At the pace I work, it would take me weeks to do all of that, by which time if I did find something wrong the place I got it from would be like, "Tough patooties, your warranty expired 3 months ago!"
In your case, if you go ahead and replace the timing components and water pump, you're already going to be giving the engine a pretty good once-over, probably more than most folks would do, so I think you'll be ahead of the game.As for lubing the engine, if you're pulling the valve covers to inspect the cams, anyway, I'd put assembly lube all over them - bearing surfaces, lobes, tips of the valves (if you can reach them), etc. You can lube all the timing components as you're replacing those. Is there a way to pre-lube the V6s? On LS engines there's a port on the front driver side of the block that you can screw a 16mm-1.5 adapter into and hook up a hose to pump oil through the engine before you start it, so that's what I did when I had to replace my LS6. If you can't do something like that, then you can at least crank the engine over with the starter for a while before you actually start it - that'll get the oil pump to do its job and circulate oil through everything while there's no load on the engine.
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