I wouldn't bother with an inline fuel filter.  It's not needed and to my knowledge is just another step to deal with when troubleshooting.

 If you really want one I'd wait until after you have everything running well, just to avoid having one more part to check if things aren't going right.

Here is the thread about fuel filters in the Technical Section.  They can cause fuel flow problems.  The nipple on the plastic filter has pretty thick walls and it drastically reduces the cross section (and flow) of the fuel.  It also is small enough that an air bubble can get stuck in the small nipple and block the flow of fuel (air lock).  There have been several members who experienced problems after installing a fuel filter.....and it is hard to diagnose why the engine won't run when you are stuck on some dark deserted road.  The fuel system has a screen on the petcock, and another one at the top of the needle/seat assembly in the carb.....most likely you won't need a third filter.
http://suzukisavage.com/cgi-bin/YaBB.pl?num=1211846392

The other issue is that the fuel system is gravity and it is operating under a tiny amount of pressure.  With less than a foot of space between the carb and fuel tank - even with a full tank there is likely less than 1 psi of pressure trying to move the fuel to the carb.

I never change the oil until after the bike is started the first time.  If you drain the oil and take the filter out - the engine won't get any oil until all the air is pumped out of the filter housing......I think it is far better to get old oil pumping than it is to be pumping air through the engine after sitting for years.  At a minimum I would leave the filter in place and just change the oil in the sump if you feel you need to.....I really don't believe waking up an engine with a dry oil filter housing is a good idea.

Absolutely put some oil in the cylinder.  Also lube the cam well when you have the head off to put fix the head cover leak.  After you get the head cover back on - squirt oil through the exhaust valve inspection port and fill up the little rectangular trough that is below the cam.....that is where the cam and rockers get lube for the initial start.

The first thing to do is make sure it runs properly.  You don't want to dig into the head only to find out it's not running right.  Then you'll have to wonder if it was messed up before you tore it apart or if it was something you did wrong.  Just my .02.