Ipsi and contralateral indications are puzzliing me for some reason.
I am following the Epicritic and protopathic pathways, but I find no common ground to saying when something is going to be IPSI or Contra EVEN before the decussation asending the neural pathway.
For example, going from the big toe to the parietal lobe (cerebral cortex) I have the sensory - discriminitive (Epi) pathway and along that line I can have cut in the PNS and CNS that blocks signals and has a CONTRA and IPSI effect. I see that in the medial lemniscus where sensory decussation is, I can have a contra effect. If it is in the dorsal columns it is IPSI. AHHHHHH!
In general, I understand that if it is before the decussation marker, it is generally COntra. If it is after, it is ipsi.
What is missing from my understanding or am I complicating it too much? 
I'm not entirely sure I understand your question. I, too, have trouble with this. One thing that I found was confusing me was what terms I was thinking in. I have to remember that the ipsi and contr are in reference to where the lesion is, not where the signal is coming from- that confused me at first. Not sure if that is any help. (On the other hand, once you get it, it's cool- I was shadowing in the ER recently, right after having an exam on this stuff, and was able to figure out where a problem was- sort of-- turned out the problem was real big and not confined to the area I thought, but it was still interesting to put the info to use).
I 'm having trouble understanding your question as well, but this is the way we were taught to determine the location of a lesion. First we define the 'level' of the lesion as in:
Supratentorial (cerebral hemispheres)
Posterior Fossa (brainstem, cerebellum)
Spinal (spinal cord, nerve roots)
Peripheral (peripheral nerves, muscles)
Multiple levels
Then we determine the 'side' of the lesion using some fairly straightforward rules depending on the level we have determined the lesion to be:
If the lesion is supratentorial then it is contralateral to the side of face/body weakness or sensory loss.
If the lesion is at the level of the posterior fossa the lesion is:
a. ipsilateral to face weakness/numbness and contralateral to body weakness/numbness.
b. ipsilateral to the cranial nerve deficit (III-XII)
c. ispsilateral to the cerebellar ataxia
If the lesion is at the level of the spinal cord or roots the rules are:
a. ispilateral to the weakness and/or loss of vibratory/position sensation.
b. contralateral to the loss of pain and temperature (except at the segemental spinal level, where it is ipsilateral)
If the lesion is at the peripheral level, it is ispsilateral to the side of weakness or sensation loss.
Determining the 'level' of the lesion can be a bit tricky but you can use things such as
aphasia/memory/behavior/seizures = supratentorial
hearing/vertigo/diplopia/dysarthria/dysphagia/ataxia = posterior fossa
neck or back pain/sensory dissociation = spinal
limb pain without back pain/loss of all sensory modalities = peripheral
These rules don't always hold true and must be taken into context of the clinical situation. There is a great book out there called Medical Neurosciences: An approach to Anatomy, Pathology, Physiology by Systems and Levels by Eduardo E. Benarroch. It gives a nice systematic approach to determining neurosystem pathology.
thanks MPP, that is what I needed is some rule to go by since I think I missed that lecture and it is not specifically spelled out in the Notes.
THe notes are great, but a few small things are missing which she covered in lecture.
That helps me spell out some general principles to go by. It helps me determine WHERE a deficit is better by following the yellow brick road.
God this stuff is hard. 
for example i found here:
Damage to the Base of the Pons
Abducens N fibers ipsilateral LMN paralysis of Lateral rectus m.
Pyramidal Tract: contralateral UMN paralysis (spastic hemiplagia due to damage to the descending corticospinal fibers)
If I understand it, the contralateral effect should ONLY happen after the decussation in the Pyramid in the latter. I can clearly see due to the atlas where the ipsi effect is limited and why, but the latter puzzles me. Apply this to your chart APP. Thanks.
Do you charge for this tutoring? LMAO 
I think the problem is that my rules are for working from the clinical signs and symptoms to find the source of the lesion. Your example starts with the lesion and asks for the clinical signs and symptoms. So just use the rules listed above backwards.
A lesion of the Pons is in the posterior fossa. For lesions in the posterior fossa you will find weakness of muscles supplied by the cranial nerves (in this case Cranial nerve VI - Abducens) ispsilaterally. Cranial nerve VI is a Lower Motor Neuron (LMN) for the muscle that abducts the eye (Lateral rectus). Lesions in the posterior fossa will also lead to weakness of extremity muscles contralaterally since the corticospinal tract decussates in the pyramids of the medulla (lower on the brainstem). The corticospinal tract is the Upper Motor Neuron (UMN) for all extremity muscles (the LMN for these muscles are in the anterior horn of the spinal cord - the alpha motor neurons). If the corticospinal tract is knocked out on one side of the pons (located in the basis pontis or the ventral portion of the pons) you will have hemiplegia on the contralateral side of body to the lesion along with the ipsilateral paralysis of some muslces innervated by cranial nerves. The spasticity and increased tone seen in UMN problems comes from the lack of innervation of interneurons and hence no inhibition of muscles. There could be other motor and sensory problems depending on the exact location of the lesion in the pons.
That was a bit wordy but hopefully understandable. To make it a bit simpler, I will rewrite rule 'a' for a posterior fossa lesion from the chart I posted eariler.
A lesion at the level of the posterior fossa leads to ipsilateral weakness in muscles of the face/head and contralateral weakness of all other muscles.
Let me know if this makes sense.