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I had root canal and cap...I still get zings and occasional bells and whistles but for the most part it is ok.
You can get systemic infections from lots of things... including root canal work.  I happen to take antibiotics prophalatically (amoxycillen "horse" dose) an hour before dental work because of existing, harmless heart murmur....if you are prone to infection, or are deeply concerned about it, discuss this option with your doctor.
However, if your first experience was essentially positive, I would recommend root canal and saving the tooth.
The key here is not to go to "hungry" dentists...ones who beat the $$ bushes for money...and there are tons of them out there.  You need a primary dentist who is honest in his/her assessment of the "savability" of the underlying tooth, who tells you honesty, who shows you the tooth root on film and discusses it with you.
And you need to find the root canal person with the best, best reputation .  There are good ones and very good ones..  plus, the crown must be perfectly molded and fitted..and re-worked.
 
I've had 4 or 5 (after a while they run together) root canals in the 
last 2 years. Your dentist should give you antibiotics for any 
infection _before_ s/he finishes filling and crowning the tooth. Is 
the tooth that hurts completed, or only partially done? If completed, 
it should not zing. Before that it might, since the root has not been 
taken care of yet. The routine is--drill out old filling, start 
cleaning the cavity. Place a temporary crown. Give 10 days 
antibiotics (I got Omnicef, since it's one of the few that doesn't 
give me gut problems, make me dizzy, etc.). Then finish cleaning out 
the cavity, get the root, fill it with gutta percha, take an 
impression for a final crown. Replace temporary crown. Go in whenever 
final crown is ready and have that placed.
 
I am a diagnosed celiac for 16 years and I have had a root canal.
 
I haven't had any trouble with it and that was 4 years ago.  I would recommend that you check the doctor out and make sure he does a lot of root canals.  The doctor that I went to, only does root canals!


If at all possible, do not have the teeth pulled. Most dentists will 
tell you it's pretty much always better to save existing teeth than 
to try to replace them (my father's a dentist, though he was in 
research and didn't practice after he got out of the army in the 
mid-1940s). Once they're gone, you can have problems such as the 
bridges coming loose, remaining teeth shifting, and resultant bite 
problems, perhaps leading to the need to remove more teeth, 
eventually get dentures, etc. (My considered opinion--Dr. Mercola 
doesn't know what he's talking about. Sorry if you think he's good--I 
personally find much of his site to be very bad medical advice.)
 
I've have three root canals and can't see any evidence that my health has been adversely effected because of them.  I know there are those out there that believe that root canals are the root of all illness (no pun intended), but my very conservative naturopathic physician does not agree with that position.  It's a tough decision, but look at it this way:  If you have the root canal,  you can always have it extracted later if you believe it's causing you problems.  When you have a bridge, that involves grinding down the two teeth adjacent to the space down to a nub then being crowned.  A root canal may be less expensive than a bridge.  I'd rather the root canal.


 
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