had to remove the side cam cover and now wont start, backfired like crazy thru carb and exhaust pipe. What position should the cylinders be in to check the cam timing. The cam timing marks lined up with the pistons at BDC. What stroke should the pistons and valves be in?

What year bike do you have?

It is a 98 just redid the valves and had to take apart the cam cover

None of that matters if you put them in correctly. If I rember correctly, the #2 cam (the one with the big gear on it) only goes in one way. Then just line up the marks as per the manual and you're good to go. Be very careful with the marks, though. You have to get your face right down there level with the cams to make sure you're right. If it's running at all, they're close. Might be off 1 tooth, though.

All of the marks are lined up correctly when the pistons are at BDC, but I am wondering if the pistons have to be at TDC when you put the cams in. It won't run at all and it backfires every once in awhile through the carb when I try to start it.

The below info I wrote when changing cams in my 04 ... but, I would think that is would pertain to your motor too:

Replacing the Cams:

Prior to replacing the cams, they should be cleaned with a spray of brake cleaner and then lubricated thoroughly with engine oil to include the cam lobe and drive gear.

The rocker arms will need to be removed in order to take the pressure off the cams prior to there removal and replacement.

Insure that the timing mark on the #5 gear (pinion gear) is pointing directly at the center of the #2 cam’s bushing ... see picture below.

http://x402.putfile.com/4/10520102388.jpg

Note: When installing each cam, the lifters can be moved slightly up into there bores with you fingers while you are installing the cams. This will allow each cam to slide all the way into the bushing in the engine case.

Cam Identification:

#1 cam (Rear Exhaust Cam)
#2 cam (Rear Intake Cam) (cam with double gears)
#3 cam (Front Intake Cam)
#4 cam (Front Exhaust Cam)

Note: The “V” markings on the cams are not used for timing purposes. Disregard them.

Install the #1 cam. Insure that the slot marking is also pointing directly at the center of the #2 cam’s bushing.

Install the #3 cam. Insure that the slot marking is also pointing directly at the center of the #2 cam’s bushing.

Install the #2 cam. As you install this cam, insure that all 3 timing marks (dots) on this cam line up with the timing slot markings on the other 3 gears (#1 cam, #3 cam and the #5 pinion gear).

Now install the #4 cam. Insure that it’s timing mark (dot) line up with the dot on the #3 cam.

All timing marks should now be alligned exactly as in the diagram below:

http://x402.putfile.com/4/10520111672.jpg

The picture below shows the cams now properly installed. Note that the mark on the pinion gear is still pointing directly at the center of the #2 cam.

http://x402.putfile.com/4/10520133636.jpg

There are some cam swap photo's here. This is what I used for swaping cams an worked fine at start up. May help you out.
http://home.sandiego.edu/~ekim/harley/tstorm/thud.html

WinXP ..... That link don't work

Anyway, the photos I posted should be all he needs. I don't think I could made it any clearer than that.

Thanks Turbota, so it seems that the piston position doesnt matter just the timeing mark on the pinon gear should be pointing at #2 is that correct?
If we were going to attempt this without removing the heads completly, just the covers to get the pushrods with no pressure should that work

If the engine is rotated with the cam gears removed ... each time the pinion gear mark points to the #2 cam bushing, the pistons will still be in the same place. It can't be '180 out' as long as the mark on the pinion gear is pointing straight at the #2 cam bushing.

You don't need to remove the heads, but the lower rocker boxes need to be removed so there is zero pressure on the cams. Might as well take the pushrods out at the same time ... takes 5 seconds since you have removed the rocker boxes.

You will have 2 shorter pushrods. The short rods go on the intakes. The longer rods go to the exhaust.

Your going to need new rocker box and rocker cover gaskets since you pulled them apart.

Ron,

Thanks that is great info I think I can get it together now !

Good luck ..... You should be fine.

Oh ya ... When installing the lower rocker box, insure the pushrods are in a fully down prior to tightening the rocker arm bolts. This will cause the least amount of spring pressure on the rocker arms prior to tightening. In high gear with plugs removed ... turning the rear wheel until both pushrods are in there lowest position will verify this.

Always torque down the 4 larger rocker box bolts before you install and tighten those smaller screws. When you start tightening down the rocker boxes, once there starts to get resistance on the 4 larger rocker arm bolts, then turn them down about a 1/4 turn at a time. This gives the lifters time to slowly bleed down as the preload is applied ... Dont want to bend the pushrods. (the rocker box will set just slightly above the heads at first, before you torque them down which gives the lifters that preload they need)