Need some technical help with cam timing....

First post here for me, I hope someone can help, or direct me to a source that can! (I can't find tech manuals here?)
Bike is a 1998 VX800. 6,000 miles . Sat for many years and when previous owner started it an exhaust valve stuck and bent.  Have replaced the valve, etc. and that cylinder now has excellent compression and no leak through the valves.  (this is the rear cylinder)
Anyway, I turned the crankshaft to TDC rear cylinder, timing mark is visible in the sight hole.. Reinstalled the cam with the "arrow" pointing forward and parallel with the head surface. This appears to be correct? (I bought a Haynes manual but it has proven to be pretty useless in this area...)
Got the bike running, but the rear cylinder backfires and pops and sputters all through the RPM range.  (carbs are cleaned and manually synched) 
I thought maybe the cam/crank relationship was 360 degrees out, but that shouldn't matter?
It really sounds like a 'retarded' cam situation...
But compression is good and valves don't hit.....
Anyone help?
Thank you in advance!
Regards, Jim