Hi,
TMR3 seems to share it's clock pin with TMR1 and I haven't really looked into what effects that has but here's what I'd try:
Code:
TRISA.4 = 1		'TMR0 CKI Pin as input
TRISC.0 = 1		'TMR3 (and TMR1) CKI Pin as input

'From Datasheet Section 11
T0CON.7 = 1		'TMR0 is ON
T0CON.6 = 0		'TMR0 is 16 bits
T0CON.5 = 1		'TMR0 clock source is EXTERNAL...
T0CON.4 = 0		'...and counts on rising edge
T0CON.3 = 1		'NO prescaler is assigned
T0CON.2 = 0		'Prescaler 1:1
T0CON.1 = 0		'Prescaler 1:1
T0CON.0 = 0		'Prescaler 1:1


'From Datasheet Section 14
T3CON.7 = 0		'Disables 16bit read/write
T3CON.6 = 0		'TMR1 is clock for both CCP's (together with BIT 3)
T3CON.5 = 0		'Prescaler 1:1
T3CON.4 = 0		'Prescaler 1:1
T3CON.3 = 0		'TMR1 is clock for both CCP's (together with BIT 5)
T3CON.2 = 1		'Don't sync with internal clock.
T3CON.1 = 1		'TMR3 clock source is EXTERNAL
T3CON.0 = 1		'TMR3 is ON
I've set the bits one by one here so that it's easier to see what each one does. Note that I haven't tested this so it's perfectly normal if it doesn't work...

/Henrik Olsson.