I have had some experience in bit banging I2C, mainly from a PC printer
port.  I think there are a few improvements that you could use.

Firstly my initialisation routine always sends a couple of STOPs, just to
try to clear the bus of any half completed communiactions.  You are getting
some kind of communications so this isn't your problem, but it is a good
idea and can save a lot of grief.

        -- init I2C lines
        procedure i2c_init is
           pin_a3_direction = input             -- clock high
           pin_a4_direction = input             -- data high
           pin_a3 = low
           pin_a4 = low
        end procedure

Secondly, your start and stop procedures always assume the state of SDA and
SCL.  A much better solution is to assume they will be in the wrong state.

ie.
Start
    SDA = HI
    SCL = HI
    SDA = LO
    SCL = LO

Stop
    SCL = LO
    SDA =  LO
    SCL =  HI
    SDA =  HI

        -- output a start condition
        procedure i2c_put_start is
           _i2c_wait
           pin_a4_direction = output           -- data low
           _i2c_wait
           pin_a3_direction = output           -- clock low
        end procedure

        -- output stop condition
        procedure i2c_put_stop is
           _i2c_wait
           pin_a4_direction = output        -- data low
           _i2c_wait
           pin_a3_direction = input         -- clock high
           _i2c_wait
           pin_a4_direction = input         -- data high
        end procedure

I had a lot of problems using your start method, especially if you are doing
multi byte commands were a second start has to be issued.

The only other thing you may want to look at is giving the slave an
acknowledge.  Your routine seems to do a 'i2c_put_ack' for both reading and
writing.  Surely you should be giving ACK's when you are receiving and
waiting for ACK's when transmitting?

        -- write one byte to specified address
        procedure i2c_write_1( byte in address, byte in d1 ) is
           i2c_put_write_address( address )
           i2c_put_data( d1 )
           i2c_put_ack     <-----should be getting an ACK from slave, not
sending it.
           i2c_put_stop
        end procedure

        -- write two bytes to specified address
        procedure i2c_write_2( byte in address, byte in d1, byte in d2 ) is
           i2c_put_write_address( address )
           i2c_put_data( d1 )
           i2c_put_ack     <----should be getting an ACK from slave, not
sending it.
           i2c_put_data( d2 )
           i2c_put_nack_stop
        end procedure