This is by no means a definitive guide. I just couldn't stand seeing everyone going into this blind like I had to do.

UPDATES IN BOLD
Here are the steps and tools I used to complete the header swap on my 1999 GS400.
I did not have a service manual to use as a guide, and I ran into a few problems which stretched the installation by several hours. I would guess that two people should be able to complete the installation within 6hrs-8hrs, given the proper tools.
Bear in mind that I’ve done my share of in-depth repairs and upgrades on past vehicles such as countless headers, head replacements, intakes, carb rebuilding, suspension replacements, etc.

TOOLS I USED:
10mm box-end/closed-end
10mm socket
12mm box-end
14mm box-end
14mm/12mm ‘distributor wrench’, each end is angled
14mm socket (6 pt recommended)
17mm box-end
17mm socket
Universal/swivel joint
Philips screwdriver
Crescent wrench
Breaker-bar or handle extension
3/8” ratchets (I had a short and a long one. The short 5”one with a pivoting head was VERY useful in the tight spots!)
Air-powered impact wrench/gun
6” extensions (2)
3” extension
2 jack-stands
Floor jack
½” drill bit
Dremel w/cutting head
Optional tools: tin-snips or cutters, pliers, long screwdriver or other prying tools for the heat shields. (remember, I didn’t jack up the engine)


Step 1 - Remove engine cover. 2 bolts, 2 nuts – 10mm socket
Step 1.5 - Unmount air sensor thing in top of air box and lay to side. 2 bolts, 10mm.
Step 2 - Remove air-inlet scoop and air-box. Philips screwdriver and 10mm socket
4 bolts, 10mm. (air-box front-most bolt only needs to be loosened)
Step 3 - Remove air-tube to throttle body/black box on top side of engine. Rubber
hoses, 2 bolts, 10mm socket, 2 large ‘hose clamps’
Step 3.5 - OPTIONAL: Unmount Power Steering resevoir, push aside. 3 bolts, 10mm
Step 4 - Jack up car and put on jack-stands. I used a spot where lower A-arm meets
Frame cross-member, and I also leave the hydraulic jack under frame under
drivers floorboard just for safety.
Step 5 - Spray all convertor bolts with penetrating fluid if you haven’t already.
Step 6 - Remove oil dipstick tube. 1 bolt, 10mm. Plug hole with paper towel or
something if you want to ensure that nothing drops in there.
Step 7 - Remove underside, 6 point structural brace. This may not be needed, but gives
more room to maneuver for acces to other bolts. 6 bolts, 14mm socket
Step 8 - Unplug O2 Sensors. Unplug connector first! See pic for detail on where the locking tab is at. I used a crescent wrench to get it out easily.
You'll need a 10mm to remove bracket holding the connector when you put it back together!
Step 9 - Remove catalytic convertors. 14mm socket, 14mm box-end, 18mm socket
(17mm =one nut only), breaker bar.(old Campbell Hausfeld air-gun wouldn’t cut it)
Step 10 - Unmount steering rack and let hang. 4 main bolts and 1 bolt for steering
knuckle/coupler, 17mm socket and 17mm box-end, and 12mm box-end
Step 11 - Unbolt heat shields. 3 bolts per shield. 10mm box-end.
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Note:
Right here you have a choice. I chose to try to remove the heat shields from their nest. This may not have been the wisest choice!! I probably spent at least an hour on each side just trying to get them out forcefully. I was using tin-snips and prying/forcing techniques. They always looked like they would almost come out, but it’s DECEPTIVELY TIGHT and the shields have odd angles on them!

An alternate method would have been to *try* to reach all manifold bolts by shifting the shield around since it does move around in there a little bit. It just didn’t look to me like that would be any fun.
Another smarter method might have been to undo the engine mount bolts from underneath and jack up the engine about 2 inches. (could be done for both sides of engine) I’ve not checked, but it seems feasible that you would want to unbolt the transmission mount bolts as well. I can’t be sure how much the engine will move when only doing one side, or w/o doing the tranny mounting bolts.
It sounds like a lot of extra work, but, in reality it’s only about 6 bolts and could save you between 1 and 3 hours of total work, manifold removal/header install included.
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Step 12 - Remove manifold bolts. Manifold will come right out. 16 nuts, 14mm socket,
14mm box-end, extension’s, ‘breaker-bar’.
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Notes:
Passenger side: 4 bolts are accessible from the top using socket and pivot-head, short handle ratchet, 4 on bottem accessible from underneath using both socket and box-end wrench.
The passenger side front pipe’s lower bolt is easily accessible using 15” of extensions and a universal swivel joint right at the socket. Access is from beneath the front of car.
Drivers side: 3-6 bolts are accessible from underneath using sockets, extensions and box-end wrenches.
The top nut on the second pipe from the front was SERIOUSLY hard for us. There is a molded in bracket for the oil dipstick tube AND the manifold has a curved lip on it (at the block) that damn near prevents access with a box-end wrench.
ALSO, the pipe from the first cylinder crosses in front of the bolt preventing most sockets from fitting in there as well. LOOK AT THIS BEFORE YOU BEGIN.
In the end, we spent a good hour here too, and finally used the 14mm/12mm ‘distributor wrench’ with the angled ends AND a pry bar to force it to stay completely and firmly on the nut. A handle extension may be required as well for leverage.
I’d love to know how others’ got this one. The short socket doesn’t clear the stud, a medium length socket wouldn’t fit in there due to the exhaust pipe.
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Step 13 - Remove old gaskets if you have new ones to install. I had new ones, but my
old ones still looked very good and re-useable.
Step 14 - Re-install everything. (I was able to assemble the headers and catalytic
convertors together outside of the car. I then put them in as a single unit
per side, no problems.}

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Note: My drivers side header would not quite slip easily over all the studs. After about 20 minutes I realized that I was not going to be able to force it into place.
When measured against the stock manifold, you can see that the bolt holes are JUST SLIGHTLY smaller, giving less “wiggle room” to go over the studs.
I drilled out the two rear bolt holes and the two front bolt holes with a ½” drill bit, oiling frequently. (10-20min) This is just slightly oversize. Now it slips into place like a glove!!

Also, I couldn't figure out why we got the nuts and bolts that we got. It was mentioned in other threads that the nuts do not fit the 4 longer bolts that were provided.
I felt that their provided shorter bolts were too short for the header to converter so
I ended up taking the 4 longer bolts from the convertor to the Y-pipe and used them up at the header-convertor flange. Then I used the new, provided , 4 longer bolts with older/used nuts for connecting the convertor to the Y-pipe.
CHECK YOUR NUTS PRIOR TO INSTALL!!! PLAN AHEAD!


Final Thought: Ensure you get adequate mating between the cat’s and headers, heeding J.Brady’s advice on the subject or my solution in the pictures below.


.

 

im praying for pics

but great writeup

 

Drivers side manifold bolt - CYL #2

 

Passenger Heat Shield - Cut Up!

 

Passenger Heat Shield #2 - Cut Up!

 

Steering rack

 

Pass. O2 plug NO REACH!!

 

O2 sensor plug2

 

O2 sensor plug4 tiewrap

 

REMOVAL NOTE: O2 sensor

 

Bolt Length Comparison

 

Catalyst tube-lip

 

Stock manifold flange

 

Stock manifold-catalytic no gasket

 

Pass. Header Flange