I've just re-built my CP Pro after a crash. I had to replace the main shaft and tail boom. I've just carried out a test flight and the heli flies, but I'm unable to lift it more than a foot off the ground whereas previously it could fly much higher. I've checked the main rotor tracking and it looks fine and the battery is fully charged.

Any idea what is causing this problem?

Some things to check first....

pitch settings - you may have too much pitch at to low a throttle possition. did you change or adjust any connecting rod lengths?
motor pinion to main gear mesh - make sure this is not overly tight, an out of round main gear can also rob power but not usually enough to inhibit flight.

if neither of these is found to be out of spec, than I would change the main motor out. It may have sustained damage in the crash.

read this thread [link]http://www.rcuniverse.com/forum/m_3131294/mpage_1/key_/tm.htm[/link]
And maybe refference sme pictures here....[link]http://www.bladecprepair.com/man_bh_upgrade.html[/link]

Then check your head suteup....top to bottom you find something out of whack, mixing arms are backwards...loose main shaft retaining collar...paddle pitch...something...