My proposal for...
Arabic Romanization: alif <a` / aa> ba <b> ta <t> tha <th> jim <j / g> ha <h`> kha <kh / k`> dal <d> dhal <dh> ra <r> zay <z> sin <s> shin <sh> Sad <s`> Dad <d`> Ta <t`> Za <z`> ayn <e` / e> ghayn <gh / g`> fa <f> qaf <q> kaf <k> lam <l> mim <m> nun <n> ha <h> waw <w / u / o> ya <y / i> alif madda <`a> ta marbuta <a / at> alif maqs`ura <a> fatha <a / aa> d`amma <u / uu> kasra <i / ii> hamza <`h / h`> For comparison look here.

Overall, it looks pretty good, but I have a few things to say: First, why do you use ` rather than a normal apostrophe? For waw, what is the difference between usage of u and o? I'm guessing that the o represents the combination of fatHa and waaw, but I'm not completely sure. Also, I'd leave h entirely out of the hamza transliteration. With your system, it looks way too much like what you use for Haa', and there simply is no h-like sound in the hamza, anyway. One thing you could do is use the regular apostrophe for this, since you haven't used it yet. What you use for ayn looks interesting, although a lot of people might mistake that for a vowel. If you want to stay away from symbols or characters with diacritics, perhaps you could use c? It's used in Somali for this sound, and Arabic transliteration sometimes uses a raised small c to represent ayn, anyway. Also, what you have for alif madda, with the ` before the vowel, could pose some problems. Fortunately, in Arabic, the form fu3laan where the madda would occur is somewhat rare, the most well-known being qur'aan, or qur`an in your transliteration. But what if there was an Arabic word where the second root is an emphatic consonant (or any one that uses `), and the second consonant is an alif madda? That would result in two ` in a row.

First, why do you use ` rather than a normal apostrophe? Well, for me it's an aesthetic choice, but it also frees up the apostrophe for other uses. For waw, what is the difference between usage of u and o? I'm guessing that the o represents the combination of fatHa and waaw, but I'm not completely sure. You'd be completely correct in your guess. Also, I'd leave h entirely out of the hamza transliteration. With your system, it looks way too much like what you use for Haa', and there simply is no h-like sound in the hamza, anyway. One thing you could do is use the regular apostrophe for this, since you haven't used it yet. Well, I had considered only using ` and omitting the hamza as an onset, but I just sorta went h crazy... What you use for ayn looks interesting, although a lot of people might mistake that for a vowel. If you want to stay away from symbols or characters with diacritics, perhaps you could use c? It's used in Somali for this sound, and Arabic transliteration sometimes uses a raised small c to represent ayn, anyway. Well, the only issue I can see with using c is that it too can be confused, as the consonant /k/, but confusing none-the-less. That would result in two ` in a row. Which I think would be wholly distinguishable.

Well, for me it's an aesthetic choice, but it also frees up the apostrophe for other uses. Ah, that's fine - just remember that in the transcription system you gave, you don't actually use the regular apostrophe. As for your use of o, that's logical, but if you want to be more consistent, you should go ahead and use e as an alternate form of yaa' - that is, when you have faTha + yaa', you get the vowel transcribed as e. Well, the only issue I can see with using c is that it too can be confused, as the consonant /k/, but confusing none-the-less. 3ayn is one of the hardest sounds to romanize. I'd prefer c over e simply because e can be mistaken for a vowel. You also have x available, I'm not sure if you want to use it though.

As for your use of o, that's logical, but if you want to be more consistent, you should go ahead and use e as an alternate form of yaa' - that is, when you have faTha + yaa', you get the vowel transcribed as e. It's a good idea...I'll give it while... 3ayn is one of the hardest sounds to romanize. I'd prefer c over e simply because e can be mistaken for a vowel. You also have x available, I'm not sure if you want to use it though. No, I surely don't want to use x for ayn, but I also don't want to use a number or only punctuation.