There is this site:
Flights:
http://www.kayak.com/flightsMake sure you click on "+/- 3 days", prices may vary for different dates, depending on God knows what. Normally, 6-7 weeks in advance is enough. Farther in advance is not necessary, and closer than 2-3 weeks to departure prices start climbing.
Un-click "Choose sites to compare" at the bottom - Kayak usually finds a better price than Expedia etc. You might find better prices on less known small local carriers not shown in Kayak, can't suggest any, maybe locals would chime in. In Europe small local carriers often have horrible surcharges for luggage and/or fly only on certain days of the week, can't say about S.A.
Playing a devil's advocate here, - why don't you register and ask a question to expats at
Chapala forum? Guadalajara is their backyard, so to speak.
Hotels:
TripadvisorCheck the reviews and photos and decide for yourself. "Sort by Rating" is not always useful, as there seems to be different "rating" depending on the price bracket, i.e. there can be 5 star rating for a simple hotel and 2 stars for some upscale place that is likely better, but people paying that much expected more, so they rated it low.
Pop-up windows on this site are annoying, but I don't know a better source.