Engine light on, 2nd gear only, no speedometer

@ 75000 mi. Same thing happened, repaired by dealer under extended warranty. Said needed new transmission speed sensor. Tranmission fluid changed by dealer every 30,000 mi. Never any slippage, shifts great and firm, above is only repair on trans. Ever. 1st time this happened it went into limp mode after a long highway run and stopping at a stop sign. This time it happened over a period time. I left work, trans in 1st gear and moving slowly and suddenly quickly shifted to 2nd gear with a bang and I noted speedometer quit working. Realizing I was in limp mode I pulled over, shut engine off, restarted and the trans and speedometer worked perfectly for several more days. There was no check engine light before or after it went to limp mode. Once in the past my battery failed and after a jump start the speedometer did not work and and didn't work until I got to a parts store and replaced the battery. I thought this was the cause again as the battery was 4 yrs. Old so I replaced it. Even with the new battery the limp mode eventually returned and finally stayed, with now the check engine light on and no speedometer. Internet says output shaft speed sensor probably bad. If I change this myself is there any special knowledge I need and does anything have to be reprogrammed (as in dealer) before it works properly? Or have I misdiagnosed my problem? Another problem is a gradually worsening exhaust leak at the engine (3.3 liter flex fuel). I can't locate it with with accuracy but it appears to be leaking around the exhaust manifolds. The dealer says it's probably the exhaust manifolds have cracked and need replacing, apparently at great expense as they said the car's too old to bother with the expense. Is this engine prone to exhaust manifold cracking, or could it be the gaskets have failed? The engine runs perfectly, always on synthetic oil with no oil consumption on 5000 mile change intervals. The body and interior are in great shape and I hate to throw it away. If the manifolds are prone to failure is there a source for new ones that won't break the bank? Thank you.