Firing order and valve timing

Hi guys, I am new to Aprilias but have had, and worked on bikes for er, too many years.

I bought a non running 2000 RSV Mille with what the owner thought was "a dropped exhaust valve, and no clutch pressure". Turns out the clutch release bearing disintegrated dropping balls all over the place and jamming one ball in the primary gear locking the engine. Only damage was to the primary drive gears which I replaced. (thanks ebay!)

My problem though is that I can't be certain how to reallign the camchain timing gears. I have downloaded the Aprilia engine manual and I also seen a few pages of the Haynes manual on this forum. They both talk about locking the engine at TDC and making sure the IN and EX marks line up, which I've done, but when I rotate the engine and observe the cam lobes on both cylinders the timing seems to be wrong.

QUESTION: When the rear cylinder is at TDC on the compression stroke (EX and IN cam lobes upwards(ish), what position should the INlet cam lobes be on the front cylinder? My old mechanic training tells me that the inlet cam should be starting to open as the piston starts going down on the front cylinder as the rear one is going down on it's firing stroke. Any body can set me straight here? I think this engine has been stripped before and I cant trust the timing marks on the gears.

Thanks guys.

IMPORTANT HEADS UP!
I finaly worked out the correct valve timing on my 2000 RSVMille. After watching the cams as they rotated through their sequence I realised that the front cylinder was 180 degrees out. This made the REAR cylinder fire on the EXHAUST stroke as the Camshaft sensor is mounted on the front cylinder.
I had followed the Hayes manual to set the timing for the camshafts. It says to set the rear cylinder first by locking the crank at TDC and positioning the cams according to their marks, then rotating the engine 60 degress counterclockwise and lock the front cylinder at TDC and position the front camshafts to their marks. THIS IS INCORRECT!!!!!! DO NOT FOLLOW THIS INSTRUCTION.

It should say to rotate the crank 420 degrees counter clockwise and lock at TDC for the front Cylinder. This places the front cylinder on the firing stroke while the rear cylinder is on the intake stroke.

After getting the bike running properly I read in this forum that someone else had the same problem and worked it out.

Cheers,

Xen.