Do you know the reason why in English we can find a lot of tanses which disappeared in the other ones? Many of them simplyfied or as I said just disappeared. It's just unthinkable to use it nowadays e.g. polish past perfect turned into simple past.
And the next problem. What's the origin of the tenses kind of present perfect? Comparing it to e.g. my native language Polish it's just something impossible to translate, for instance:
Eng: I have been working all day,
Polish: I worked all day ( the only way to express the meaning)
Eng: Have you ever been to London?
Polish: Were you ever to London?
These examples show that in each case Present Perfect is replaced by Past Simle and Present Perfect even have never existed in Polish.
The truth is, English has hardly any tenses at all. It has a true past tense and pieces of a true present tense. But that's it. For whatever reason, English has gradually whittled away at complex verb conjugation over the centuries.
However, in language, you rarely "simplify" one aspect of grammar without counterbalancing it by "complicating" some other. If your verb no longr has any intrinsic way of expressing that it is (for example) first person plural future, it will need strict syntax and "help" from other words: "we will go." The base verb (in this situation, an infinitive) "go" needs both "we" and "will" to express any grammatical meaning.
So English tends to resort to all kinds of verbal constructions where other languages rely on verb inflection tto convey time, person, number and mood.
Well, I suppose the answer to your first question is that languages change at different rates... Polish and German and French have used the perfect for things which English still uses the simple past for. But even in English different dialects change at different rates: American English and various kinds of British & Irish English have retained the simple past in cases where Standard English (the sort you learn and is normally found in edited published books) uses the perfect. On the other hand, Australian English and New Zealand English have already started using the perfect in cases where Standard English doesn't allow it, like narratives, or with certain adverbs (this is a similar path to what German and French have already taken, apparently). I don't find this odd at all—I'm an Australian, and while I think I've written this in Standard English, it's entirely possible someone else will find half a dozen uses of past perfects that aren't a part of the Standard.
(BTW: I don't mean to imply that AusE and NZE are more evolved than Scottish English and American English: different languages take different paths, and it might be that it turns out the past participle was just a plesant deviation in other dialects, and they end up going back to the simple past.)
As to your second question: It's not completely clear where it came from, and your examples and language are a bit confused. The present participle is -ing, which comes from an earlier confusion between the present participle (-ende) and a verbal noun form (-unge/-inge) of Old English. The continuous aspect is formed with "be V-ing", as in present continuous "I'm working", past continuous "I was working", past continuous perfect "I've been working all day". There are example of a comparable (but optional) use dating back all the way to the earliest records of English, so it could always simply have been "be" and the present participle (which was given particular grammatical functions later on in the development of English), but alternatively it might've been from "be" + "on" + the verbal noun.
Your second example is of the so-called present perfect. It likely derives from a resultative construction (i.e. thinking about the result of an action, you "have" the result).
Note the terminology can be a bit confusing, particularly when thinking cross-linguistically or about dialects which have generalised the present perfect. What's called the "perfect" in other languages is the "present perfect" in English ("I've done it"), which is confusing because (a) a past-tense form of the verb is used and (b) in expresses the fact that something happened before now. It's used because (in the Standard) it means that there is some continuing relevance. It stands in contrast to the past prefect: "I'd done it", which has the past-tense form of "have", and (in the Standard) expresses similar meanings to the present perfect but relative to some points in the past.
(BTW to JJM: English never had more than two tenses. In fact, Proto-Germanic is reconstructed with only two: Past and non-past. What English has lost is its various moods, but it more than makes up for that in its numerous analytic aspects.)
I hope none of that's too confusing! Ask further, and I might be able to help.
I said: "... it's entirely possible someone else will find half a dozen uses of past perfects that aren't a part of the Standard".
I meant to've said:"... it's entirely possible someone else will find half a dozen uses of PRESENT perfects that aren't a part of the Standard".