Smoke on start up is usually a sign that the valve stem oil seals need replacement as they are allowing oil to seep down the stems when the TTR is left standing.
The bigger Wiseco pistons such as on my 325 can give the same symptoms. Blue smoke on start up that soon clears and no oil used during running. My assumption is that the piston expands sufficiently once warm to give the correct operating clearances.
The fact that you have lower performance may indicate that the engine may be low on compression. The most usual causes are worn piston rings (or piston/bore) and/or valves not seating properly.
To fit new valve stem oil seals requires taking the head off so my suggestion would be to take the opportunity to check the piston/barrel and fit new rings at the very least, then strip out the valves, de-coke them, lap them back in and fit new VSOs.
Only after you have refitted the valves do you check and adjust the valve clearances.
So you would be looking at buying, at the very least, VSOs, head & Base gasket set and a new ring set.
Before you start the strip down, after you have taken the cam cover off, check the cam chain for wear and replace if necessary.
The ticking noise could be piston slap, cam chain or valve noise all of which can be resolved during the refurb.
Wow thanks for the wall of text Brian! That is a very comprehensive explanation.
I checked, and my bike still has the original base gasket! Never opened once. And it has 175k on it! I will crack the bike open this weekend and do the clearances at least. Getting the other replacement parts will take a while though.