the little rubber caps by the injectors are perished and loose. Are they vacum take offs and do they have to be sealed ?

If you mean Nr 17
http://www.realoem.com/bmw/showparts.do?model=0503&mospid=47865&btnr=13_0515&hg=13&fg=15
then, yes, they have to be sealing and intact. But you should definitely notice them being damaged with your motor running bumpy, since they would give false air...

They are a vacuum take-off point, and as Alex has said, they do have to be sealed. You'll find that they simply slide onto the metal flange with only a small amount of effort. Replacements can be obtained from any good auto spares shop. There are several sizes available (but only one for your BMW) so take one along with you if you are replacing them. There are only three on the throttle body rack that are capped with the fourth and rear-most vacuum point being connected to the fuel pressure regulator.

OK thanks for the help..............my next problem on my long neglected bike is a very stiff clutch.

The cable is Ok but the actuating arm has proved very reluctant to move freely even after lots of penetrating spray.

I have had no luck in drifting out the pivot pin which i believe has two roller bearings .

If the clutch splines were dry would this be noticable at the clutch lever ?

The bike spent at least 3 years lying on its side in the Andalucian sun !

un Saludo

Not necessarily. The clutch splines have nothing to do with the operation of the clutch actuation. The actuating arm at the back pushes a pin that will push away a spring disk that normally holds the floating and the stationary parts of the clutch pressed together with the friction disc clamped in between. This friction disk slides over the splines, so no direct contact.
You really should try to get the actuater arm to move freely. The clutch will operate a lot easier and the strain on the clutch cable (an chance of breakage!) ill be a lot less.

There are two needle bearings in the arm, but regretfully standard no grease nipple. Try it carefully, lots of penetrating poil, bit of heat maybe.Some have damaged the gearbox by breaking of one of the fixture points.

On the 85 RT I had for while the clutch arm was stiff as hell
the bike had been laid up for some years
I got it off eventually without causing 'collateral damage' to the housing
and the shaft and needle rollers were bone dry and rusty
All a bit knackered really
I knew You can buy new arms and shafts from motobins or motoworks in the uK which have grease nipples fitted ( stainless shafts too I think)
(Just checked motobins site, £52 plus VAT plus P&P)

As it was freebie I was robbing parts off and due for eventual disposal I cleaned up the shaft as best I could and drilled and tapped a hole, fitted a grease nipple and gave it plenty.
Not a bad bit of bodging, it worked well and saved me having a left arm like Popeye and a right arm like Olive Oyl