Sounds like your nearly there....grey smoke well usualy blue is a sign of retarded timing. as long as your sure you have the pump drive gear in the correct place....only turn the pump 1mm at a time and test....keep advanceing the the motor sounds a bit knocky under load....back off the timing or retard till the knockiness just goes....spot on.
 
Just wanted to give the update all is now good I have been using the old girl as a daily bus for the last 4 weeks or so.. very little smoke, allmost like a modern motor!
I am doing about 25 miles each way to and then again home... loving it...

What I did, stripped off the timing gear, pulled out the injection distributor pump.
Set a timing disc on the crank and a dial guage on the no1 exhaust tappet.

I did a 720 degree timing diagram as a linear timeline and plotted the milestones, timing marks valve lifts an start of opening and closing, PE tdc etc. On flywheel and then carefully reasembled the timing gear.

There is a vague bit of explanation in the haynes manual that becomes clear when you turn the engine and check for each milestone in turn as it occurs, bar a very slight difference between the peak exhaust and peak inlet all looked very good apart from timng could only be either 3 degrees advanced or about 5 degrees retarded because of pulley manufacture or spurious cam grind! I did consider making a variable timing pulley for the camshaft to get it more accurate but reigned that thought in and assembled again. I opted for 3 degree advance b.t.w.
Injection timed back in and it was time to fire her up...
First turn she burst into life, smooth ( as a 2.25 ltr diesel can be) warmed up, great,
Test drive no smoke, pulls well, and all has been great since.
Oddity though, when I've done about ten miles all seems to smooth out and she settles down starts to pull more rattles less it is quite noticable

I love it, if you see a rag top S2a on the road from York to Tadcaster at commuting times holding the traffic up give me a wave and a honk...
 
Just wanted to give the update all is now good I have been using the old girl as a daily bus for the last 4 weeks or so.. very little smoke, allmost like a modern motor!
I am doing about 25 miles each way to and then again home... loving it...

What I did, stripped off the timing gear, pulled out the injection distributor pump.
Set a timing disc on the crank and a dial guage on the no1 exhaust tappet.

I did a 720 degree timing diagram as a linear timeline and plotted the milestones, timing marks valve lifts an start of opening and closing, PE tdc etc. On flywheel and then carefully reasembled the timing gear.

There is a vague bit of explanation in the haynes manual that becomes clear when you turn the engine and check for each milestone in turn as it occurs, bar a very slight difference between the peak exhaust and peak inlet all looked very good apart from timng could only be either 3 degrees advanced or about 5 degrees retarded because of pulley manufacture or spurious cam grind! I did consider making a variable timing pulley for the camshaft to get it more accurate but reigned that thought in and assembled again. I opted for 3 degree advance b.t.w.
Injection timed back in and it was time to fire her up...
First turn she burst into life, smooth ( as a 2.25 ltr diesel can be) warmed up, great,
Test drive no smoke, pulls well, and all has been great since.
Oddity though, when I've done about ten miles all seems to smooth out and she settles down starts to pull more rattles less it is quite noticable

I love it, if you see a rag top S2a on the road from York to Tadcaster at commuting times holding the traffic up give me a wave and a honk...
Good work! Homegrown methods are often the best way forward with these.
 

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