1973 RT3 in a fresh rebuild. I’ve put 500 miles on it and all is good except for bubbles in the clear oil line from pump to motor sometimes. This injection pump has me befuddled (further). I look down at the clear line to the motor and sometimes it’s full of bubbles and not oil. I’ve been putting some oil in the gas tank just to keep it from seizing. I’ve put new seals in the pump- no change. I’ve made sure it’s adjusted properly. 
I thought maybe the flow was too slow so I’ve blown air backward into the oil tank. Because all I get when I drain the tank is a pitiful stream. Maybe that’s correct, I don’t know.  
I can only figure my flow from the tank is insufficient (not likely since it doesn’t take much flow I’d think), or the pump is sucking air from somewhere. But from where? Maybe air in the line to the
motor is normal, but I doubt it. And I can’t figure how it’s getting in the system. 

Will be an interesting subject this. Probably why the use black lines so you can't see the bubbles. I'm talking off the top of my head without a pump in front of me but i think the bleed screw is only halfway up the pump body so will always have air in the pump even after bleeding. If the bike falls over off the side stand & you find it the next morning does the pump get air in from say a half empty oil tank not covering the pipe while on its side. I don't know. Keep premix for a bit & sit the feed pipe uphill & over into a glass jar & run it up playing with the cable wheel to alter the stroke & see what happens. Any chance your clear hoses are sneaking air in at the fittings. Do you have the miniature ball & spring in the outlet union--not that it would cause air, just stop gravity feeding into the motor. Someone else's turn now!!--DEET is the pump man & i'm sure he'll put us right.

Are you also running larger diameter clear hose?   Most is.  Original hose is tiny which is much less likely to "show" air.  You can still get plenty of oil flow through a larger tube and not have the tube full. 

Hello Murfalert, 
 Since you’ve driven it 500 miles here’s one way to check how the autolube system is working. Divide the amount of gasoline put in the gas tank by the amount of oil put in the oil tank. I tend to initially fill oil tank halfway up the window and run a little premix until trust that level in tank is dropping. 

Ha, never thought of that, but if its done 500 miles it must be safe, me thinks. I guess its using oil out of the tank.

Thanks for the inputs. I haven’t measured what has left the tank, but it’s easy to prime the line by hand turning the wheel so it’s definitely able to pump. 
I like the theory about too large of a line, though my mind isn’t good enough at physics to really understand the consequences. The amount of oil pumping at smaller throttle openings is minute, and maybe the system isn’t tight enough to maintain a hydraulic-like full line that just pushed the new small amount through. While it doesn’t drain back past the check valve some air may be getting in. 
I’m still not sure but I’ll look for smaller line. I think DEET sells the correct stuff but I really want clear so I can worry more. 
Murf

Just in case , 
I did read on an English based forum about the possibility that if you re-use the old clear oil lines from tank to pump the plastic can be very hard and the push on pipe at the tank can draw air when its running and vibrating ...... Worth a thought perhaps , but maybe you've changed out that line ?
Regards
Bill

I discovered recently that Lowes sells very small diameter transparent fuel line. In a red or yellow color but it is transparent. I think it is for gas powered weed wackers.

O'Reilly's Auto Parts (Advance or some other name in parts of the country) has tiny translucent line in their "Prime Line" lawn and garden section.  

Yamaha still sells the original.  

If you are somehow getting air at hose fittings one issue is clamps...  hard to get tiny clamps that work right and zip ties leave a gap.  Using factory line and clamps is best for that reason too.  

There is no check valve at the cylinder...  it's at the pump.  Nothing to keep that line from draining except "capillary action"...  a tiny tube with oil tends to stay full and not drain easily if one end is "blocked" like it is here connected to pump check valve.    

Then there's flow...  you won't keep a horizontal 3 foot diameter water pipe full with one end open and a flow of 2 gallons a minute...  most of the pipe will be full of air but the flow will still be 2 gallons a minute.  Size that pipe down to the appropriate diameter, maybe 3/4 inch, and the pipe will stay full while delivering the 2 gallons a minute.  


 

Great thinking guys- thanks! I put some weed eater fuel line on from pump to jug. It’s not really clear, but a light yellow. It seems to be fine now. I no longer see bubbles; I assume because the slow flow can keep this line full. And for the ultimate test I filled up an almost empty fuel tank and rode with no problem. 
I appreciate the thought and time for input from y’all.

As a side note; I noticed it lean on the main jet. Pulled it to find a piece of dirt lodged in the main jet. It seems I’ve tried hard to seize this thing- but alas, it’s running well.

Murf