It's easy. I was in the same position as you last week. It's definately easier if you have someone helping you out when you go to seat the cylinder over the piston rings.
Couple of tips:
If you are going to install a HV oil pump with it, have a impact driver and you may need a flexible drill shaft to drill the hole for the oil passage if you can't get the cylinder stud out.
Lay the bike onto it's left side when doing the HV pump, it makes it easier to get the shift assembly back together.
When doing the oil catch and spacer rings on the piston, put the catch ring in first (the wavey one) then slide a spacer down from the top, then the bottom. Be sure to put pleanty of
clean oil all over everything.
Have a local shop seat your valves, unless you have a valve spring compressor. Ask them to lapp the valves too.
Beware of high prices to have this done. I went to a local Honda shop and at first they told me it would be 120.00. 8O When I raised the BS flag on his ass, he then said 70.00. 8O I went to a friend of a friend and he charged me 15.00.

( Don't ever go to Jim Walker Honda in S. Daytona, they're a rip off!)
Don't forget to loosen the cam chain tensioner before you put the cam sprocket on. ( I forgot and it drove me nuts for a while)
Buy a clutch nut socket from Classic.
http://hondaminitrail.com/XR50.html
It will save you some time and effort. and you wont mar up the nut with a screwdriver. :wink:
There's a bunch of great info right here on PM, just use this:
http://www.planetminis.com/modules.php?name=Forums&file=search