Sorry i left the discussion for so long but i was doing a bit of holidaying over the weekend.
Apologies for the diode setup mistake. As Tonytech said it needs to be reversed biased in parallel with the coil.
As far as the leisure battery situation goes, with my usage pattern a normal car battery is a better bet. I tend to run the van at least once a week for long enough to fully charge both batteries. If i'm ever parked up for long enough to really discharge the 2nd battery (so the interior lights are dimming) i'll try and run the engine for about 15-30 mins to give the 2nd battery a hand until i next need to do a bit of driving.
The problems using car batteries as a 2nd battery will only really appear if the battery is sitting in a discharged state for a period of time. Once the charge nearly runs out on a normal battery the internal plates start corroding due to galvanic action and damage occurs. This process isn't particulary quick so as long as you put a bit of charge on the battery before too long then the damage is minimal. If you forget to turn the sidelights off at night and wake up to a flat battery you can jump the van and re-charge the battery without any real damage to the battery. If the van will be sitting unused for a long period then fully charge the batteries and disconnect the earth straps.
If your batteries are discharging themselves when you're not using the van then you've got a problem somewhere. You can check this pretty easily.
First, with the engine and all equipment in the van switched off, disconnect the earth strap of the battery you want to test. At this point, i like to tap the connector of the earth strap against the -ve terminal of the battery just to ensure there's not a major problem. If you do this and get big sparks, then you've either left something on or there's a big problem somewhere. If you connect a meter to a setup in this state there's a good chance you'll kill the meter. A few little pin pricks of light are ok.
Next set your multimeter up to read current. On most meters this involves plugging the test leads into different sockets than you would to read voltage. Start with the highest current rating on your meter and touch one lead to the connector on the earth strap and the other lead to the -ve terminal on the battery. The reading on the meter should be below 0.1A. If it is then set the meter up to read the lower of the current readings and connect the terminals to the same place. Depending on what equipment (alarm, immobiliser, central locking, etc) got installed on the van will determine how much current is leaving the battery, but on my van i'd be worried if was over 10mA and ideally it should be well under 5mA. Higher values means that even with the key out and the doors locked your battery is discharging.
Something else was mentioned in an earlier post that illustrated a problem that quite a few people are having that could appear to indicate a faulty battery but could actually be something else.
using an alternator is not going to fully charge a battery. As the voltages converge the current getting into the battery gets less. As a "rule of thumb" you will only get about half the AmpHour capacity out of a battery
While it's true that when the voltages converge the current going into the battery gets less, i don't entirely agree that you only get 1/2 the Amphour capacity from a battery charged by an alternator. Intelligent chargers merely regulate the voltage so the most efficient current flow is delivered to the battery at any given point. Lead acid batteries are amazing flexible and can accept a vast range of charging currents with neglible loss in capacity. Intelligent chargers are more suited to the more "prima donna" type of batteries such as Ni-MH or Li-ion which have an stupendously high capacity in a tiny space (which scares the hell out of me). Alternators are designed to output 14v (about 1v above the open circuit cell voltage of the battery) so the battery can get almost fully charged during a decent journey.
Electrical cables have resistance that's proportional to their length ie longer cables higher resistance. In an electrical circuit the higher a components resistance then the more voltage is developed across it. This is why in almost all cars the battery is close to the alternator and starter.
Imagine that a car has a 20cm run of cable between the alternator and battery. The alternator is producing 14v and the voltage at the battery is 13.9v. This means that there's a voltage drop of 0.1v in the cable.
Now imagine in a van that the cable, battery and alternator are the same but instead there's a 2m run from the alternator to the battery. This means that there will only be 13v developed at the battery as a full 1v is lost in the cabling.
If 13v is being developed at the battery and the open circuit cell voltage is about the same then the battery isn't going to get anywhere near fully charged.
As has been mentioned previously the alternator's on our vans are just plucked from cars so aren't designed to cope with this extra cabling distance. When the vans were new then this probably wasn't such a problem as the new cabling had a low enough resistance so the losses were negligible. 15 years on the resistance of the cabling has increased and the voltage at the battery has dropped.
Again this is easy to check. Start the engine then set your multimeter to voltage measurements (make sure you do this or the meter is going to come to a violent end in the next step) and measure the voltage being developed at the alternator terminal. Just touch the red wire to the main alternator terminal and the black to the metal on the alternator body. Make a note of that and then measure the voltage being developed across the batteries on the battery terminals themselves. Any difference between the alternator voltage and the battery voltage is the cable losses.
An acceptable loss of 0.5v has been mentioned in previous threads. To be honest 0.5v would get the battery nearly fully charged on a long run but i'm slightly obsessive over cable losses so i re-wired my van. If you own a petrol van then you can probably make a big improvement on the voltage drop just by running a direct cable from the alternator terminal to the main terminal on the starter motor. If you want to do this make sure you disconnect and secure the earth straps on both batteries before re-wiring.
You don't need special cable. If you can get hold of some 13amp mains cable and splice the live, neutral and earth together you'll get a fairly high current cable and should notice a big difference at the battery.
On the subject of draining the main battery by starting the engine with a deeply discharged 2nd battery and a split charge circuit i'm afraid that it again comes down to the cabling. If you're getting nearly the full alternator voltage at both the main and 2nd battery with the engine running then you'll never drain the main battery. The alternator will hold the voltage at a level so the 2nd battery gets all it's charge from the alternator and the main battery will charge at a slightly slower rate. Personally i don't have my split charge circuit fused (to be honest if you know the cabling's ok then i don't see the point). I'd strongly recommend against a diode seperation charging system for the 2nd battery. The voltage drop across a forward biased diode is going to severly limit the voltage that can be developed across the 2nd battery.
Another point mentioned was starting currents. Even if you take into account the mechanical losses i don't think that you'd get anymore that 200-300A continous current for the starting motor if the engine is healthy (800A could occur as a peak when the solenoid engages). My reason for overspecing is that at a small premium to myself i can drastically reduce the stress on my starting system by ensuring that it gets almost all the power to start the engine when i turn the key. And it'll last longer than the van. It's worth noting that it looks like VW used the same starting cable for the 2m run that it would use on a 30cm run in a car.
Although i have no hard evidence for this i can guess about the setup of the electronics in DJ engines using 80's electronics as a guide. The current draw for the electronics on DJ's should be almost neglible (no more than an amp plus the fuel pump). They should also be resistant to voltage drop. The control circuits in the ECU will almost certainly run on 5v switching 12v outputs. Both these voltages will be regulated so as long as the cabling isn't broken the engine will run. As the supply also feeds the HV side for the spark plugs it's almost certainly filtered for spikes as well. I could be wrong about this so this is not to be taken as fact.
Once again, i apologise for such a long unwieldy post. I'm leaving the country again tomorrow so maybe this thread will be able to die.
Dave
PS : Popeye - The eber's have an undervoltage protection in them. Assuming the fans blowing, try the fuel pump and failing that the glow plug.
- so a good idea to let go of that key quickly when it jams 
