Workin' on the street

["Joseph M. Shaw, II" <MikeIIDC@domain.elided>]

Okay, I appreciate everyone's sympathy that I got based on the rules for
moving cars around my neck of the woods, but now I've got an even better
story!  I had noticed that one of my rear tires was beginning to get a
little low yesterday, so I went and filled my air tank and filled it
up.  It honestly wasn't even very noticeable how low it was, but I
didn't want to take any chances of having it go completely flat and give
the neighborhood any fuel to hate me and my Scout any further.  Well, I
walked out this morning to find the tire completely flat!  Either this
was the quickest developing not-so-slow leak I've ever seen, or someone
saw me air it up and decided to help some of it back out!  Either way, I
filled it again today, but upon returning home from work tonight (I'm a
bartender so I get home around 3:00 AM) it was completely flat again. 
This one I can understand, as I'm sure its level of flatness from the
last time tore it off of its bead a bit.  But now I know someone from
the neighborhood is going to throw some kind of fit and I'll probably
get a note from the local parking authorities on my car tomorrow. 
However, it is supposed to be clear tomorrow-no rain-so I'm skipping the
first day of my new Quarter at school and working on the beast some
more.  Hopefully, before I get in any real trouble I'll have it together
and running again.  So the moral of the story is:  No matter how
bad/weird/decrepit your living situation, if you have so much as a
driveway, thank your lucky stars!
Now, the question.  I have removed the heads to clean out the cylinders
and piston heads.  Is there anything I must do before reinstalling
everything.  I'm cleaning everything, but have done as little as
possible to change the set-up of anything, simply removed things to get
them out of the way and set them in the back of the truck.  I would love
to have the valves reworked, but it appears that with the current
problems that is completely out of the question.  If I clean out the
cylinders, and put everything back together exactly as it came apart,
should everything be okay-knowing that the engine was running before
disassembly (It was misfiring/bucking, but started and ran-never
completely cut out, but was undriveable for more than ten minutes at a
time.)  Or is there something I absolutely must do before reassembly?
All of your knowledge is greatly appreciated!
Thanks!
Michael