You have to read those extra PIP sections carefully.
(a) Command difficulty is "any of"
(b) is on its own so no problem
(c) Unresponsive, mixed or forced marching troops is "For each of"
(d) Difficult evolutions is "If 1 or more of"
(e) Irregular clumsiness is " ... and either"
(a), (d) and (e) could all have used "any of" without changing the meaning. However many of the criteria you meet, you still only pay 1 extra PIP for each lettered heading.
(c) is the odd one out, the only one which can make you pay more than one extra PIP.
So to answer the original question: No it's only 3 PIPs because wheeling and moving short are both the same extra PIP.
And yes, halting clumsy irregulars is 2 PIPs (but note the various exceptions that allow you to do it for 1 PIP, particularly Irregular LH(S) that are impetuous but not clumsy so can normally halt for 1PIP).