I've not joined in this thread before now because I'm really confused about some of the crucial that has a bearing on the OPs rights and what they can reasonably expect in this case.
1) Was this a booking for a true package with Lowcost acting as a Tour Operator?
If there was an ATOL number attached to the booking then it was, if there is no ATOL number attached then the odd's are that it was a so-called 'dynamic' package and the duty of care one can expect is a good deal less tha with a 'proper' pacakge.
2) Or was this booked with them acting as a Travel Agent?
The fact that the OP seems to have a full beakdown of costs suggests that this was the case (you wouldn't usually get this with a 'proper' package), therefore, in which case it was a 'dynamic' package and this is little better than going DIY in terms of the duty care that can be expected from the TA. Yes, they were less than helpful in not being more specific about the transfer time but there is no dispute about the OP being clear from the beginning that they were booked to fly into Sofia and not Bourgas and when booking a DIY or a dynamic package I think that there is much more onus on the booker to check these things out for themselves as well.
3) Was the original booked transfer that was waiting at Bourgas, booked by the TA or the OP?
If it was booked by the TA and paid for as part of the total bill, then they have done the decent things by refunding the taxi fare and hence still providing the OP with a transfer at the same original and agreed price in both directions. If it was booked direct and separately by the OP then the onus was on them to ensure that they booked it for the right arrival airport. Either way, I don't think there's much of case for expecting Lowcost to refund both the original transfer cost and the replacement taxi fare. If it was booked by the TA in error then it is reasonable to expect them to pay for any associated expenses eg the cost of phone calls and they seem to have agreed to this on proof of costs which the OP says they can provide.
I think that the case with regards to a refund and/or compensation for missed nights in the hotel is more contentious and less clear cut. If the OP arrived at the hotel before that days check-in time and had immediate access to the room and had continued access to the room after the usual check-out time on their last day, then I don't think that they stand much chance of challenging this. It is not regarded as a 'lost night' by the travel industry. This comes up time and time again with regard to night flights even on full pacakages. There would only be a case if the OP arrived after check-in time on the day after the room was booked for and similarly had to leave it by check-out time on the day before the last booked night.
There is always a world of difference between what we think a TA or TO should feel morally obliged to do and what they are actually required to do by the law. On the basis of the information that we have been given so far, confusing as it has been at times, I suspect that Lowcost have gone a long way towards complying with the law and any further financial recompense is going to largely depend on their good will rather than their legal obligations. If I missed any crucial information that suggests otherwise I'm sure that someone will point it out to me!
SM