Yes, seems I have you confused good.

Disregard what I have posted above for the heater hoses. On the length of the drivers side radiator pipe, yes that is too long on the 4 cyl car and will need to be either shortened or replaced with a V6 one.
There are 2 ways to hook the heating lines up correctly. First would be to remove that passanger side pipe on the frame rail and replace it with the proper pipe for a 87-88 V6 car. The second would to be to cut that pipe on the bulkhead at it's highest point, or removing the pipe at the quick connect fitting down low at the bottom of the engine bay and then use heater hose to connect it to the thermostat housing on the V6 engine ( what you have circled in pic #1 ). Then remove what's left of that pipe from the engine bay and frame rail. For either of these you will need to remove the nipple fitting from the water pump and stick a pipe plug in there.
I think that by using the existing pipe on the frame rail and modifiy the connection to the under car heater pipe it would be more work, also that would route the coolant through the heater core backwards. This would work, but would also chance creating an air pocket in the heater core, which you don't want. So let's forget the earlier discussion of connecting the water pump to the frame rail mounted pipe.
The outlet from the heater core on your 87 is that pipe / hose that connects to the passanger side radiator pipe. This you can leave as it is.
Pic # 2, you'll end up removing that pipe, or a part of it.
Pic # 3 This is the air feed fitting for the EGR sensor. The V6 cars have a series of tubes bolted to the bulkhead. The fitting in pic 3 hooks to the smaller of the 2 bulkhead pipes, the hose in pic # 5 connects to the other end of the pipe. Pic 3 and 5 eventually get connected.
Some people don't bother to connect the hose from the EGR sensor and leave it open to the atmosphere inside the engine bay. This may not be any worse than having it hooked up as the feed fitting on the bottom of the air filter canister as it draws unfiltered air with the stock setup. You can decide which is the worse of the 2 evils for yourself.
Pic 4 looks like the hose for the brake booster, it gets hooked to the pipe in pic 7.
Pic 6, yep that goes to the PCV valve, there is a moulded rubber elbow that holds the PCV valve and connects to the plastic pipe. The end of the PCV valve sticks in the rubber grommet in the valve cover. if you don't have this piece, i will send you one, it's the least i can do for confusing you.
Pic 7, that grommet in the valve cover is where the breather tube plugs in. There is a 8 inch or so steel pipe that connects that grommet to the air boot between the air filter canister and the throttle body. I have these parts too if you need them.
8, there are only 2 hoses to the transaxle. The short one with the 180° bend in the steel pipe connects to theupper fitting on the transaxle. The longer one gets looped through a small bracket on the end of the transaxle and connects to the bottom fitting. it is looped to prevent the cooler lines from draining back into the transaxle wihen the engine is off.
I appoligise for mis-guiding / confusing you earlier. Sorry!
jel