I have a 2000 xr 80,we put new piston and rings in.Timing marks were lined up but is there a way to fine tune timing?

Hello epsom...you really should purchase the shop manual so you could see the illustrations and the step by step procedures on how to align timing marks and properly gap your piston rings. Plus so much more info that you are going to need to do the job right. Plus the manual has the torque specs. and the sequence---There is not enough room here to give you all the info u will need. Here is a link for the manual online, you might can find it a bit cheaper on Amazon. i hope this helps.

http://cgi.ebay.com/ebaymotors/Honda-XL-XR-125-200-Motorcycle-Service-Repair-Manual-/260718595181

clean the carb there are some tiny holes in the xr carb that can corrode closed if if the bike sits for a time
fit a new plug
check the valve clearances
put the ignition plate back were it started

Backfiring through the carb isn't a timing issue unless you're firing at BDC (180 degrees out).
or have bad/missing/cracked piston rings / hole in the piston.
I mean, correct me if I am wrong, but that thing IS a 2 stroke, right?

Valve timing is done with the piston at Top Dead Center. The cam lobes should be pointing downward. There will be a mark or marks on the cam gear for alignment of the gear. If only one mark, it should be at the top and inline with the centerline of the crankshaft. If two marks, they sholud be parallel with the surface of the cylinder. Any slack in the timing chain should be at the carb side. When the cam gear is in the proper position, rotate the cam slightly to line up the screw holes for mounting. After mounting, remove the spark plug and turn the engine over by hand to be sure the setting is correct. If the crankshaft locks up it is because the piston is hitting a valve. Re-do the cam timing. Please rate my answer. Thanks.

The diagram below should work for you. Put the piston on TDC. the OHC cam gear will have a single mark or may have two marks, see below. Be certain the front side of the chain is taut when mounting the gear. The cam chain tensioner keeps the back side taut.

By "all timing marks seem to be right", are you talking about the timing marks on the alternator rotor or the camshaft timing marks? A 1985 model is a pretty old bike. If it has never had a timing chain or the adjuster guides replaced, you may need to address this issue. Not only do you need for the ignition timing to be correct, you need the camshaft timing to be correct as well.

In your problem line, you stated that you had fuel, and spark. You need three things to get any engine to run, fuel, spark, and compression. Do a compression check on the engine. If the compression is low, it won't start either. Three things can cause low compression. Bad rings, improper camshaft timing, and valves not seating properly.

If you want to get the bike running again, I would suggest you do a "top end job" on the engine. Pull the head and cylinder. Measure the cylinder for wear and bore for a new piston if necessary. Replace the rings. Have a valve job done on the head at a local machine shop. When you put it back together, do so using a new timing chain and adjuster slides. You'll be surprised at what a "New" engine feels like. Good Luck!

I assume you are talking about the cam timing. If so, then you first turn the engine so that the "T" mark on the flywheel lines up with the index mark in the timing hole cover. This places the piston at top dead center (TDC). Now position the camshaft so that the cam lobes are both facing downward. Align the two marks on the cam sprocket with the cylinder head cover gasket surface (making sure the piston is still at TDC). Install the two bolts through the sprocket and screw them into the camshaft. Done.

you have to put the piston at the top and the sprocket and crank at the bottom hope this helped

Put the piston at TDC (Top Dead Center) by lining up the timing marks on the flywheel and stator. Put the cylinder head back together with the cam installed so the high points of the cam lobes are pointing kind of downward. Pull the cam chain taught on the front side of the engine. Put the chain on the cam gear such that, when bolted to the cam, the index mark or marks are in the proper position.

The proper position depends on what markings are on the cam. Some bikes have a single mark; an arrow, a straight line or an "O". The mark should line up with the center-line of the crankshaft. If the cam has two marks opposite each other, the lines should be parallel with the gasket surface. You will need to rotate the unbolted cam left or right just a bit in order to match up the bolt holes to the gear holes.

Can I get a “very helpful” rating on this answer?

re-strip top-end and remove scuffing marks from piston using 400# and then 600# wet n dry paper. recheck piston to cylinder clearance is correct, re-assemble checking ignition timing, fuel bowl level and inlet manifold "O" ring.