Couple of peeps have already done this so thought I'd do a write up of the steps as I got round to this today. Thanks to Jason Kruys and Stubeedoo for their tips
If you don't want to remove the pipework and would rather just install a bypass - then check this out: http://www.e46zone.com/forum/topic/53120-egr-and-breather-valve-upgrade/
Note, this DIY was done on a 330D with the earlier type of engine. If you own a later engine than my 2002 184hp engine, you will need to code out a warning light on the dash, otherwise you are lucky and won't get any warnings
If you have simply bypassed the EGR using the Allard or a.n.other kit, you may eventually run into other issues. Personally I found my kit never really formed a tight seal, it leaked slightly causing a build up of pressure and a lot of rough idling. So a complete removal of the EGR was required, I was inspired to do this by Jasons' experience: http://www.e46zone.com/forum/topic/45142-jasonkruys-330d-vert/page-2
To perform the delete, the job is very similar to this link: http://www.bimmerforums.co.uk/forum/f91/e46-330d-thermostat-ac-water-pump-drive-belt-replacement-t103035/
Step 1 - Remove the engine covers using a 5mm hex bolt or allen key
Step 2 - Undo the vortex fan shroud. Firstly undo the screw on the drivers side using a torx 25 bit, then remove the plastic clip on the passenger side. I used a small screwdriver to gently pry out the centre pin, then my handy trim removal bits to lever out the pin and the larger plastic socket
Step 3 - Undo the vortex fan. Use a 32mm vortex fan spanner to hold the thinner bolt closer to the engine and a regular 32 mm spanner to slowly undo the main bolt. This bolt released a bit of pressure on my car when I made the first turn, it needs to be turned clockwise to be removed.
Step 4 - Remove the cable box on the drivers side attached to the shroud. Gently lift the shroud and fan out and Unclip the smaller set of cables. Remove the fan and shroud carefully, taking care not to damage the radiator
Step 5 - Move the air pipe away from the MAF by undoing the two Hex 5 bolts. I found it difficult to access the bottom bolt and so used my bendy screwdriver, but an allen key will work too:
Swing this pipe to the left to give you access to the EGR connection to the manifold below it
Step 6 - Now you can start removing the EGR pipework. First undo the two Torx45 bolts at the manifold
This is what the bolts look like
The guide I linked to above says the central EGR unit has one 10mm hex bolt, I found in fact there were three bolts. To remove these I had to use my hinged screwdriver
At this stage it got a bit tricky and messy. To be able to remove all these bolts, I had to remove the EGR thermostat, but to remove this I had to loosen and shift the position of the vacuum pipe. I also "borrowed" some clips from my wifes kitchen, don't tell (!) So I could temporarily clamp the coolant hose
I had to remove my EGR pipework in bits which also revealed how dirty it was
The following pic shows how much gunk was getting stuck at my EGR bypass I fitted only 2 months ago.
The final bit is removing and blocking off the coolant pipes feeding the EGR stat. I used silicon bungs, thanks for the tip Jason. http://pages.ebay.com/link/?nav=item.view&id=190892513049&alt=web. I bought two 18mm black hose ends and some jubilee clips. I was originally planning to add some sealant but got lazy, they seem to be doing the job. When you undo the bottom egr hose, coolant gushes out so be ready to just pop one of the ends onto the pipe stub. I found just pushing it on held back the tide, giving me time to slip the jubilee clip on and tighten it.
Finally you end up with all these bits
Step 7 - Now you need to put your blanking plate by the manifold. Its a bit tricky to line up the plate, washer, cage and bolts but doable. The 'cage' thing at the left gets in the way, and frankly you don't need it but I couldn't remove it. I found though if you wiggle it towards you it comes forward quite a bit, allowing you to easily put one bolt through it, the plate and gasket. I could then slide the whole bit back into place and begin to tighten the bolt into its receiving end. I then put the bottom bolt in and tightened both as much as I could.
I used this plate, http://www.ebay.co.uk/itm/181216025801?_trksid=p2059210.m2749.l2649&ssPageName=STRK%3AMEBIDX%3AIT, some have used this plate, http://www.ebay.co.uk/itm/321170494662?ssPageName=STRK:MEWNX:IT&_trksid=p3984.m1439.l2649 and some have machined their own.
Finally, put the fan and shroud back together. I struggled to put the shroud back in, took a lot of wiggling. On a plus note there is now more free space and so it was easier to put the fan back together.
Your engine bay now looks something like this
Once everything is connected, check your coolant level and top up if required. Then bleed the coolant, if you google this there are plenty of guides. (slowly and just a quarter turn or so) loosen the one remaining coolant bleed screw you have left, and run the car. When coolant leaks from the screw, then job done, tighten the screw. These plastic screws are fragile, so be gentle!