Hmmm. Interesting country. I've 'done' Baja California - not cycling but climbing mountains and exploring deserts.
Some general observations that may be helpful:
Potholes can be BIG, even in the middle of major towns. The most interesting roads are dirt/gravel, but can be severely washboarded, so check your fillings before you go. If you hire a car, go for 4WD, as you will definitely want to travel down these roads if you wish to explore properly, and the 2WD won't be insured for it. You'll need ingenuity and good driving skills, too, for all the washed-out sections you have to negotiate. If the car needs a good going over before you hand it back, take it to a manned car wash, where approximately 10 staff will be on hand to really give it the works.
If it rains, you are quite likely to find arroyos that are normally bone dry 350 days a year running with water, and many dirt roads will cross these, so watch out. You will also encounter numerous unsigned and unpainted road humps. These will launch you quite high if driving and you don't spot in time, so enjoy the ride and wince for the suspension!
Locals tend to favour enormous American pick-ups and 'SUVs'. Even the poorest-looking back-of-beyond shack is likely to have one or more of these outside. Driving standards weren't too bad in my experience.
You'll encounter numerous carcasses by the roadside - dogs, horses, cattle, coyotes - all probably bloated and honking to buggery and most unpleasant to cycle/walk past. No fluffy-animal syndrome in Mexico!
Try to wild camp if possible, should that be your thing. This is safer than you'd imagine, and you can find some marvellously deserted, moderately remote spots with unspoilt vistas without much difficulty. Plenty of stunning-view-through-tent-flap-at-dawn opportunities for added value (although the sun's heat on the flysheet will propel you out of your sleeping bag with guaranteed alacrity each morning). No British mudbath camping problems - the ground will be rock hard. Make sure you avoid camping on tracks - can be tempting when searching for a site late in the day, but getting mown down in the night by a pissed-up local is a real possibility.
Remember that the average height is quite short - many situations that might provide plenty of headroom for Mexicans will have northern Europeans cracking their nuts. They think nothing of stringing barbed wire across gateways/passageways at European head-height, so watch out at night when it might not be obvious.
Don't trust the maps. You will find roads on the wrong side of valleys, and other serious errors. Lonely Planet will have the usual complement of inaccuracies and out-of-date entries, so keep a notebook to report these back.
Do not wander around scantily clad at night or when intoxicated. Falling on a cactus patch will likely render you seriously injured.
Be amazed at the number of staff in public service institutions doing absolutely nothing. Manana, as ever, applies. Be prepared for astonishment on the part of vendors at a simple request for a stamp.....

Phrasebook essential.
Mexican food gets rather tiresome after a while. There's only so much tortilla-type wrap variation before the novelty wears off, so best to do two-days-on/one-day-off.
If keen to cycle, mountain bikes and a 4WD will be essential to get you to the good bits.
Definitely worth the effort of getting off the beaten track. Good luck...and report back in due course.....!?